United are now 20 games unbeaten in the division - the second longest run without defeat in a single Premier League season after the Arsenal Invincibles of 2003-04 - but as with so many of their previous performances this campaign, they were never totally convincing.
Edwin van der Sar, Rio Ferdinand and Wayne Rooney were rested as United, who changed six players from the
fortuitous 2-1 win at West Brom on Saturday,
including a first league start for defender Chris Smalling, gave a nod to their third round FA Cup tie at home to Liverpool on Sunday.
With nine wins and a draw from their home games it was no surprise that United enjoyed long spells of dominance in possession, though Stoke did not help themselves by carelessly giving the ball away on the rare occasions they got hold of it.
Berbatov was first to threaten as he toe-poked wide after Ryan Giggs's heavily deflected shot fell into his path, but United only had to wait a little longer to score.
It was the 27th minute when Berbatov sent Nani away down the right and his low cross into the six-yard box was met by a spark of genius from the Mexican Hernandez, who flicked the ball impudently between his legs and into the corner of the net.
Stoke would have been grateful for the half-time whistle and whatever manager Tony Pulis said during the break paid immediate dividends as they attacked the United goal with gusto at the start of the second half.
Tuncay headed a Huth cross wide before the Turk turned creator, finding space on the left to whip over a pinpoint cross that Whitehead glanced into the bottom corner for his second goal of the season.
Perhaps scored too soon, because United flew at the Potters' rearguard with a renewed vigour, roared on by the majority of the 73,401 crowd.
Whitehead almost went from hero to villain as his crazy backpass on the halfway line put Berbatov through, but the Bulgarian was denied by a fine Ryan Shawcross recovery tackle, before Huth brilliantly shackled Hernandez in the box with the Mexican sniffing another goal.
Smalling happy with performance
Just after the hour mark, United once more nudged ahead, again thanks to a moment of individual inspiration.
Hernandez crafted a yard to find Nani on the edge of the box and he turned inside on to his left foot, hitting a rocket of a shot that flew past Asmir Begovic's despairing dive.
Stoke tried to fight back for a second time, but it was United who looked more likely to score as the game wore on, Hernandez blazing over after great work from the hugely impressive Rafael down the right.
Ferguson will expect improved displays as the season wears on, but few could argue that United are now in control of their own destiny.
90:00+3:14 The game is over, as the referee blows his whistle.
90:00+1:29 Luis Nani produces a cross.
90:00+0:09 The ball is swung over by Ricardo Fuller, save by Tomasz Kuszczak.
87:14 Dean Whitehead gives away a free kick for an unfair challenge on Michael Owen. Direct free kick taken by Darren Fletcher.
85:32 Ryan Giggs takes a outswinging corner from the left by-line played to the near post. The referee blows for offside. Indirect
free kick taken by Asmir Begovic.
85:09 Short corner taken by Luis Nani from the right by-line, The ball is crossed by Rafael Da Silva.
84:29 Unfair challenge on Jermaine Pennant by Patrice Evra results in a free kick. Direct free kick taken by Asmir Begovic.
80:46 Ryan Giggs produces a left-footed shot from inside the area that clears the crossbar.
77:44 Substitution Michael Owen joins the action as a substitute, replacing Javier Hernandez.
77:44 Substitution Michael Carrick comes on in place of Darron Gibson.
74:49 Substitution Ricardo Fuller on for Kenwyne Jones.
73:18 The ball is swung over by Luis Nani, save by Asmir Begovic.
69:15 Shot from deep inside the area by Javier Hernandez goes over the bar.
67:52 Substitution Jonathan Walters on for Rory Delap.
67:52 Substitution Jermaine Pennant on for Matthew Etherington.
66:47 Javier Hernandez is caught offside. Asmir Begovic takes the free kick.
65:51 Javier Hernandez takes a shot. Robert Huth gets a block in. Dimitar Berbatov takes a shot. Dean Whitehead gets a block in.
64:35 Rory Delap concedes a free kick for a foul on Patrice Evra. Free kick taken by Tomasz Kuszczak.
62:50 Danny Collins gives away a free kick for an unfair challenge on Luis Nani. Free kick taken by Ryan Giggs.
61:03 The assist for the goal came from Javier Hernandez.
61:03 GOAL - Luis Nani:Man Utd 2 - 1 Stoke Luis Nani gets on the score sheet with a goal from just outside the penalty box to the top left corner of the goal. Man Utd
58:48 Dimitar Berbatov is ruled offside. Asmir Begovic takes the free kick.
57:58 Outswinging corner taken right-footed by Luis Nani, clearance made by Andy Wilkinson.
57:20 Matthew Etherington delivers the ball.
57:09 Matthew Etherington delivers the ball.
55:44 Luis Nani takes a shot. Blocked by Marc Wilson. Outswinging corner taken left-footed by Ryan Giggs played to the near post,
Headed effort from inside the area by Chris Smalling misses to the left of the goal.
54:13 A cross is delivered by Rafael Da Silva.
51:41 Darron Gibson takes a shot. Asmir Begovic makes a save.
51:17 Free kick awarded for an unfair challenge on Javier Hernandez by Robert Huth. Darren Fletcher takes the direct free kick.
49:48 Assist on the goal came from Tuncay Sanli.
49:48 GOAL - Dean Whitehead:Man Utd 1 - 1 Stoke Dean Whitehead finds the back of the net with a headed goal from inside the six-yard box. Man Utd 1-1 Stoke.
48:26 Danny Collins challenges Luis Nani unfairly and gives away a free kick. Direct free kick taken by Luis Nani.
47:47 Free kick awarded for a foul by Marc Wilson on Darren Fletcher. Free kick taken by Chris Smalling.
46:59 The ball is crossed by Robert Huth, Headed effort from inside the area by Tuncay Sanli misses to the left of the target.
46:43 The ball is crossed by Matthew Etherington, clearance by Darren Fletcher.
46:04 Darren Fletcher challenges Tuncay Sanli unfairly and gives away a free kick. Direct free kick taken by Ryan Shawcross.
45:01 The game restarts for the second half.
45:00+1:06 The first half comes to an end.
44:12 Darren Fletcher produces a cross.
41:53 The ball is sent over by Rory Delap.
40:45 Shot by Matthew Etherington from outside the box goes high over the crossbar.
Correction - 37:03 Javier Hernandez takes a shot.
37:03 Javier Hernandez takes a shot. Blocked by Robert Huth.
36:25 The ball is swung over by Ryan Giggs.
34:53 Luis Nani produces a left-footed shot from outside the penalty box and misses left.
33:13 Unfair challenge on Matthew Etherington by Rafael Da Silva results in a free kick. The free kick is delivered left-footed
by Matthew Etherington from left channel.
32:29 Marc Wilson takes a shot.
29:43 Robert Huth gives away a free kick for an unfair challenge on Dimitar Berbatov. Luis Nani has a direct shot on goal from the
27:41 A cross is delivered by Andy Wilkinson, save made by Tomasz Kuszczak.
26:15 Assist by Luis Nani.
26:15 GOAL - Javier Hernandez:Man Utd 1 - 0 Stoke Goal scored by Javier Hernandez from inside the six-yard box to the bottom right corner of the goal. Man Utd 1-0 Stoke.
23:40 Danny Collins concedes a free kick for a foul on Luis Nani. Direct effort from the free kick comes in from Ryan Giggs.
23:05 The ball is sent over by Ryan Giggs, clearance by Robert Huth.
21:33 Ryan Giggs takes a shot. Blocked by Ryan Shawcross. Dimitar Berbatov produces a right-footed shot from close range which goes
wide of the right-hand upright.
21:18 Rafael Da Silva produces a cross, Robert Huth manages to make a clearance.
20:24 Free kick awarded for a foul by Rory Delap on Nemanja Vidic. Tomasz Kuszczak restarts play with the free kick.
18:10 Inswinging corner taken by Luis Nani from the left by-line.
15:45 The ball is swung over by Darron Gibson, clearance by Andy Wilkinson.
15:07 Foul by Tuncay Sanli on Darren Fletcher, free kick awarded. Darren Fletcher takes the free kick.
13:41 Corner crossed in by Ryan Giggs, save made by Asmir Begovic.
13:21 Darron Gibson takes a shot. Blocked by Rory Delap.
12:11 Danny Collins crosses the ball.
11:20 The offside flag is raised against Javier Hernandez. Asmir Begovic takes the indirect free kick.
9:58 Andy Wilkinson takes a shot. Nemanja Vidic gets a block in. Corner taken by Matthew Etherington from the right by-line played
to the near post, Nemanja Vidic makes a clearance.
7:27 Javier Hernandez challenges Dean Whitehead unfairly and gives away a free kick. Matthew Etherington crosses the ball in from
the free kick, clearance by Darron Gibson.
6:42 Unfair challenge on Marc Wilson by Rafael Da Silva results in a free kick. Asmir Begovic restarts play with the free kick.
6:36 The ball is delivered by Darren Fletcher, Robert Huth makes a clearance.
5:09 Darron Gibson produces a right-footed shot from long distance which goes wide right of the goal.
4:05 Matthew Etherington concedes a free kick for a foul on Rafael Da Silva. Free kick taken by Luis Nani.
2:51 Foul by Rafael Da Silva on Matthew Etherington, free kick awarded. Danny Collins crosses the ball from the free kick left-footed
from left wing.
2:18 Luis Nani crosses the ball.
1:51 Dimitar Berbatov takes a shot. Blocked by Ryan Shawcross.
0:27 A cross is delivered by Javier Hernandez, save by Asmir Begovic.
0:00 The match gets underway.
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