Hidetoshi Nakata and Kevin Nolan clinched victory for Bolton late on after Chris Kirkland's heroics looked to have earned a point for West Brom.
Albion's keeper saved well from Kevin Davies, Nolan and Henrik Pedersen.
Diomansy Kamara, who was felled by El-Hadj Diouf, wasted West Brom's best chance, blazing a second penalty over the bar after his first was disallowed.
Nakata made Albion pay with a 20-yard strike into the bottom corner and Nolan fired in a low drive to secure the win.
The Trotters started brightly with Diouf hooking a volley wide from the edge of the box while Kirkland comfortably dealt with Stelios Giannakopoulos' curling free-kick.
He then reacted sharply to save Davies' first-time shot from Nakata's low cross with his outstretched left foot.
But it was Albion who should have taken the lead after Kamara was bundled over in the box by Diouf.
The Senegalese international picked himself up and coolly sent Jussi Jaaskelainen the wrong way with the resultant spot-kick.
However, referee Mike Dean ordered the penalty to be taken again as West Brom striker Geoff Horsfield had encroached into the box before the kick was taken.
Jaaskelainen guessed the right way for the re-take, but it mattered little as nerves got the better of Kamara and he blazed high over the bar.
Bolton's early threat dissipated somewhat as the half wore on - West Brom's three centre-backs, led by Darren Moore, repeatedly repelling the home side's aerial bombardment.
But it was hardly surprising that Bolton's best chance of the half should come from a deep ball towards the back post.
Kirkland, for once, misjudged Pedersen's cross, allowing Abdoulaye Faye to head back across goal but Nakata's volley from six yards smashed into Giannakopoulos on the line and deflected over.
However, the Albion stopper was on hand to push Nolan's powerful header over the bar just before the interval.
After the break, it was more of the same as Albion rarely threatened, while Bolton struggled to make the most of their possession.
Neil Clement cleared a Pedersen effort off the line after Kirkland had taken the pace off the shot and Diouf blasted the rebound over the bar.
Kamara wasted Albion's two best chances, screwing his first effort wide from a tight angle.
And on the hour, he took advantage of some hesitant Bolton defending to fashion an opening but blasted straight at Jaaskelainen.
Nakata finally broke the deadlock with his first goal for Bolton - driving in a low free-kick after Martin Albrechtson had fouled him.
And Nolan capitalised deep into injury time after his attempted pass to Giannakopoulos rebounded back to him on the edge of the box and he drilled a right-foot shot past Kirkland's despairing dive.
Bolton boss Sam Allardyce:
"Nakata's overall play is beginning to get better and better and we will look to make his move permanent in the January transfer window.
"If he continues like this, he will be a good capture for us.
"He is not that used to the Premiership but he took up the challenge and produced his quality."
West Brom boss Bryan Robson:
"The referee has lost us the game. I told him that but he blanked me - the decision on the free-kick was an absolute joke.
"It is annoying as a manager when the players have played with a lot of discipline and were comfortable.
"Then the referee makes a bad decision to give them a free-kick from which they scored - obviously he felt a bit of pressure from the Bolton fans."
Bolton: Jaaskelainen, O'Brien, Ben Haim, N'Gotty, Pedersen, Faye, Giannakopoulos, Nolan, Nakata, Diouf (Fadiga 84), Davies.
Subs Not Used: Walker, Jaidi, Borgetti, Fernandes.
Booked: Nolan, Diouf.
Goals: Nakata 81, Nolan 90.
West Brom: Kirkland, Curtis Davies, Moore, Clement (Earnshaw 84), Albrechtsen, Greening, Watson, Carter, Robinson, Kamara, Horsfield (Kanu 64).
Subs Not Used: Scimeca, Chaplow, Kuszczak.
Booked: Albrechtsen, Carter.
Ref: M Dean (Wirral).