A David Luiz goal immediately after the interval ultimately proved decisive as Wanderers slipped to defeat against Champions League chasing Chelsea at Stamford Bridge.
Following a determined and gutsy opened 45 against a Chelsea side that contained familiar faces Gary Cahill and Daniel Sturridge, Brazilian Luiz struck on 47 minutes.
The Trotters endeavoured to find a route back into the game as Nigel Reo-Coker dragged Wanderers' best chance wide.
Though Didier Drogba doubled the lead with a header from a corner and as the Whites committed numbers forward, Frank Lampard found space to volley home a third late on.
Owen Coyle made one enforced change to the starting line-up that had previously helped Wanderers progress to the quarter-finals of the FA Cup at Millwall seven days earlier.
Mark Davies missed out with a hamstring strain. Darren Pratley took his place in a five man midfield that was flanked by Tuncay Sanli and Ryo Miyaichi.
Though the Japanese youngster saw little of the ball inside the early exchanges with the hosts launching a series of dangerous attempts to breach Adam Bogdan's goal.
They invariably came through livewire Sturridge, as he skipped away from a number of tackles down the right flank before cutting in on his left foot forcing Bogdan into a smart sprawling save.
For all Chelsea's possession and pressure, Wanderers defended resolutely with Tim Ream and David Wheater making countless timely interceptions snuffing out any sense of danger.
Ashley Cole sliced an effort wide from distance whilst Wanderers' only real attempt of note inside the opening half saw Miyaichi fizz an effort over the crossbar at the near post following a clever cutback from Tuncay.
Chelsea were left somewhat frustrated as referee Mike Oliver brought the opening half to a close.
There was every reason to be optimistic as the second half got underway, but the Whites were soon undone by a relatively straight forward goal just minutes after the restart.
Inexplicably central defender Luiz assumed possession on the edge of the Bolton before taking a couple of touches and planting a curling effort into Bogdan's far corner.
It was a frustrating way to start the half, but Coyle's charges responded well in search of an equaliser.
Reo-Coker saw the ball fall fortuitously at his feet on the edge of the area following an attempted pass to David Ngog, but the Wanderers skipper snatched at his effort that fizzed wide of Petr Cech's goal.
Whilst Wanderers enjoyed plenty of possession in the Chelsea half but never really carved out any clear cut chances.
Luiz clipped the outside of Bogdan's post from a corner kick before Drogba saw a long range effort catch the top of the crossbar.
Though Ivorian Drogba wasn't to be denied, as he rose high in a packed penalty area to head home Lampard's inswinging corner despite the best attentions of Miyaichi on the back post.
Bogdan then expertly saved from Michael Essien's long distance drive, as Coyle shuffled his pack introducing Marvin Sordell and Chris Eagles
in an attempt to find a route back into the game.
Though in the end it was to prove fruitless, as Lampard made sure of the points in the final minutes with a well-taken volley at the back post following Juan Mata's precise cross.
Next up for Wanderers is a trip to the Etihad Stadium to face title-chasing Manchester City.
Chelsea: Cech, Ivanovic, Cole, Luiz, Essien, Ramires (Obi Mikel 88), Lampard, Mata, Drogba (Torres 76), Sturridge (Kalou 80), Cahill (Unused substitutes: Turnbull, Malouda, Meireles, Bertrand)
Wanderers: Bogdan, Steinsson, Wheater, Ream, Ricketts, Muamba, Reo-Coker, Pratley, Miyaichi, Tuncay (Eagles 75), Ngog (Sordell 66) (Unused substitutes: Jaaskelainen, Robinson, Knight, Klasnic, Boyata)