The performance was ragged at times and the Blues' customary possession game crumbled in the face of the Trotters' more physical display.
Chelsea 1-0 Bolton Wanderers: As it happened
However, Carlo Ancelotti's boys battled to earn three points and create a clear gap at the top.
Bolton pressed and harried Chelsea in the early exchanges and had the better of the first 20 minutes, although the Blues came closest to getting the ball in the net when a Didier Drogba free-kick was punched clear by Jussi Jaaskelainen straight onto the head of Salomon Kalou but he guided it wide.
The breakthrough came two minutes before half-time when Drogba zinged in a superbly weighted out-swinger from the left, allowing Nicolas Anelka to head home from close range with Jaaskelainen stranded.
Chelsea's physios were kept busy at half-time. There had been an anxious moment in the eighth minute when John Terry hurt his right foot tackling Matthew Taylor, but he carried on playing to the relief of watching England manager Fabio Capello.
Left-back Yury Zhirkov was also in the wars. A clash of heads with Bolton striker Kevin Davies left the Russian wearing a large bandage until he could be stitched up.
For Bolton, Chung-Yong Lee proved slippery and elusive on the right flank, but Chelsea, with three changes to Saturday's Wembley starting line-up, did enough, even if it was all hands to the pump at the end.
Midfielder Deco was rested as Ancelotti continued rotating his squad, while in-form Florent Malouda, who had scored five times in the previous four games, and Joe Cole came on as second-half substitutes.
Bolton had a handball shout against Chelsea captain Terry waved away by referee Lee Probert and the Blues came a whisker away from doubling their lead when Frank Lampard beat the keeper in the 79th minute only to see his shot ricochet off the post.
Substitute Johan Elmander came closest to levelling for Bolton with a far-post header and Cole had a chance to wrap it all up in stoppage time but the ball got caught under his feet.