Stephen McManus scored his first goal for Middlesbrough as Plymouth's survival hopes suffered a blow.
Boro took the lead against the run of play as defender McManus headed in Barry Robson's free-kick on 22 minutes.
The Pilgrims responded well, but Alan Judge missed a penalty after a handball by Jusin Hoyte - his spot-kick being saved by Boro keeper Brad Jones.
Plymouth pressed after the break, but Jonathan Franks' long-range strike deep into injury-time sealed Boro's win.
The Pilgrims may count themselves unfortunate to lose after an even match, but defeat leaves them four points adrift of safety with just four league matches left.
Saturday's game against Watford - who are only out of the drop zone on goal difference - now takes on huge significance, particularly as Plymouth's following two matches are against Newcastle and Nottingham Forest.
Middlesbrough, meanwhile, retain an outside hope of the play-offs, with Gordon Strachan's men six points off the pace.
Plymouth boss Paul Mariner: "If there is a bigger game than a six-pointer, then Saturday's game [at Watford] will be it.
"We are still in there with a fighting chance and while we have that we will be doing all we can to stay up.
"We are in control of our own destiny, we can only affect things that are in our hands."
Middlesbrough manager Gordon Strachan: "It was one of those end-of-season games with a wind blowing about and a bobbly pitch, two teams desperate for points, both wanting a win.
"It got a bit hectic out there. I would have liked to see us pass it about a bit more but conditions dictated we couldn't.
"We did all right at times. It's a good result for us and a bit unfortunate on Plymouth. They missed a penalty but we have done that two or three times this season so I know what that feels like.
"It was a good save by Brad, he's a good goalkeeper."
90:00+4:21 The referee signals the end of the game.
90:00+3:06 The assist for the goal came from Barry Robson.
90:00+3:06 GOAL - Jonathan Franks:Plymouth 0 - 2 Middlesbrough Jonathan Franks fires in a goal from outside the area low into the middle of the goal. Plymouth 0-2 Middlesbrough.
90:00+2:26 Reda Johnson takes a shot. Save by Brad Jones. Corner taken right-footed by Yannick Bolasie from the left by-line to the near
post, clearance made by Barry Robson.
90:00+1:11 Handball by Damien Johnson. Barry Robson takes the free kick.
90:00+0:22 Corner taken left-footed by Barry Robson.
88:52 Outswinging corner taken by Yannick Bolasie from the right by-line, Stephen McManus manages to make a clearance.
88:15 Chris Killen challenges Damien Johnson unfairly and gives away a free kick. Damien Johnson sends in a cross, Karl Duguid takes
a shot. Chris Killen gets a block in.
87:31 Effort on goal by Scott McDonald from inside the box misses to the right of the target.
86:49 Free kick awarded for an unfair challenge on Barry Robson by Jamie Mackie. Brad Jones takes the free kick.
85:31 Inswinging corner taken by Yannick Bolasie from the left by-line, clearance made by Barry Robson.
84:49 Free kick crossed left-footed by Damien Johnson, clearance made by Rhys Williams.
84:49 Booking Rhys Williams is given a yellow card.
84:41 Yannick Bolasie fouled by Rhys Williams, the ref awards a free kick.
Correction - 82:29 Handball decision goes against Chris Killen. David Stockdale takes the direct free kick.
82:29 Substitution Jonathan Franks is brought on as a substitute for James O'Shea.
82:29 Handball by Chris Killen. David Stockdale restarts play with the free kick.
80:15 Foul by James O'Shea on Karl Duguid, free kick awarded. David Stockdale restarts play with the free kick.
77:16 Chris Killen challenges Chris Clark unfairly and gives away a free kick. Damien Johnson takes the free kick.
76:23 Substitution Chris Killen is brought on as a substitute for Lee Miller.
74:49 The free kick is swung in left-footed by Onismor Bhasera, save by Brad Jones.
74:49 Booking Barry Robson goes into the book for unsporting behaviour.
74:46 Booking Booking for Karl Duguid for unsporting behaviour.
74:08 Barry Robson challenges Karl Duguid unfairly and gives away a free kick.
73:20 Substitution Rory Fallon on for Alan Judge.
72:07 Scott McDonald is penalised for a handball. Direct free kick taken by Damien Johnson.
70:04 Unfair challenge on Lee Miller by Reda Johnson results in a free kick. The free kick is swung in left-footed by Barry Robson.
Rhys Williams delivers the ball, Scott McDonald takes a shot.
67:35 Inswinging corner taken by Barry Robson, Lee Miller has an effort at goal from close in which goes wide left of the goal.
63:27 Substitution (Middlesbrough) makes a substitution, with Scott McDonald coming on for Leroy Lita.
62:22 Outswinging corner taken right-footed by Alan Judge from the right by-line, Reda Johnson produces a header from deep inside
the six-yard box that clears the crossbar.
61:32 Substitution Yannick Bolasie is brought on as a substitute for Bradley Wright-Phillips.
60:45 A cross is delivered by Alan Judge, save made by Brad Jones.
58:49 Outswinging corner taken from the left by-line by Barry Robson, clearance made by Reda Johnson.
58:34 Barry Robson takes a shot. Save by David Stockdale.
57:26 Jamie Mackie has an effort at goal from outside the box which goes wide right of the goal.
57:09 The official flags Leroy Lita offside. David Stockdale takes the indirect free kick.
55:02 Unfair challenge on Joe Mason by Kyle Naughton results in a free kick. Karl Duguid restarts play with the free kick.
52:00 Jamie Mackie takes a shot. Blocked by David Wheater. Corner taken right-footed by Alan Judge, clearance made by Barry Robson.
47:46 Onismor Bhasera concedes a free kick for a foul on Julio Arca. Free kick taken by Julio Arca.
47:26 Headed effort from deep inside the area by Lee Miller misses to the left of the goal.
46:55 Karl Duguid gives away a free kick for an unfair challenge on James O'Shea. Direct free kick taken by Kyle Naughton.
45:01 The second half kicks off.
45:00+2:58 The match has reached half-time.
45:00+1:57 Leroy Lita fouled by Bondz N'Gala, the ref awards a free kick. Direct free kick taken by Kyle Naughton.
45:00+0:34 Alan Judge challenges Julio Arca unfairly and gives away a free kick. Barry Robson delivers the ball from the free kick left-footed
from left channel, Bondz N'Gala makes a clearance.
43:10 Alan Judge produces a cross, Headed effort from inside the area by Reda Johnson misses to the left of the target.
42:50 Corner taken short by Alan Judge.
41:41 A save by Brad Jones from penalty by Alan Judge. Plymouth 0-1 Middlesbrough.
41:41 Booking Justin Hoyte goes into the referee's book.
41:14 Alan Judge takes a shot. Justin Hoyte is adjudged to have handled the ball.
40:36 Rhys Williams challenges Jamie Mackie unfairly and gives away a free kick. David Stockdale restarts play with the free kick.
40:00 Booking Leroy Lita receives a yellow card for dissent.
37:34 The ball is sent over by Karl Duguid, Reda Johnson makes a clearance.
34:07 Alan Judge produces a cross.
33:47 Julio Arca takes a shot. Comfortable save by David Stockdale.
31:16 Reda Johnson concedes a free kick for a foul on Leroy Lita. Direct free kick taken by Rhys Williams.
29:31 Foul by Bradley Wright-Phillips on Stephen McManus, free kick awarded. Kyle Naughton restarts play with the free kick.
26:16 Free kick awarded for a foul by Jamie Mackie on David Wheater. Direct free kick taken by Justin Hoyte.
24:07 Bradley Wright-Phillips takes a shot. Brad Jones makes a comfortable save.
22:52 Free kick awarded for a foul by Julio Arca on Onismor Bhasera. Onismor Bhasera restarts play with the free kick.
21:32 Barry Robson provided the assist for the goal.
21:32 GOAL - Stephen McManus:Plymouth 0 - 1 Middlesbrough Stephen McManus finds the net with a headed goal from inside the penalty area. Plymouth 0-1 Middlesbrough.
20:47 Justin Hoyte fouled by Reda Johnson, the ref awards a free kick. Barry Robson sends in a cross,
17:08 Inswinging corner taken right-footed by Alan Judge, Jamie Mackie has a headed effort at goal from deep inside the area missing
to the right of the goal.
15:58 Foul by Leroy Lita on Karl Duguid, free kick awarded. Direct free kick taken by Karl Duguid.
14:31 Reda Johnson challenges Lee Miller unfairly and gives away a free kick. Direct effort from the free kick comes in from Barry
13:39 Leroy Lita challenges Bondz N'Gala unfairly and gives away a free kick. David Stockdale takes the free kick.
12:24 Alan Judge takes the outswinging corner, Headed effort from inside the area by Reda Johnson misses to the right of the goal.
12:09 Bradley Wright-Phillips takes a shot. David Wheater gets a block in.
11:28 Barry Robson takes a shot from just inside the penalty box which clears the bar.
9:43 Unfair challenge on Leroy Lita by Damien Johnson results in a free kick. Barry Robson crosses the ball from the free kick
left-footed from right channel, free kick awarded for an unfair challenge on Reda Johnson by Leroy Lita. Free kick taken by
8:47 Corner from the right by-line taken by Alan Judge, David Wheater makes a clearance.
8:21 Jamie Mackie takes a shot. Blocked by David Wheater.
5:53 Unfair challenge on Lee Miller by Damien Johnson results in a free kick. Barry Robson produces a shot on goal direct from
the free kick.
3:42 Corner taken by Barry Robson played to the near post, save by David Stockdale.
3:20 James O'Shea takes a shot. Reda Johnson gets a block in.
2:07 Leroy Lita is ruled offside. David Stockdale restarts play with the free kick.
0:00 The game begins.
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