With Manchester United defeating Everton, the Blues are now five points adrift with three games to play.
Jose Mourinho rested Frank Lampard, Joe Cole and Didier Drogba ahead of Tuesday's Champions League semi-final clash at Liverpool.
Chelsea, with the lion's share of possession early on, found the Bolton rearguard stubborn.
Only a Salomon Kalou run on ten minutes into the area caused the visitors any panic, but unfortunately Andriy Shevchenko misread the ball completely and the danger was cleared.
But Bolton took the lead on 19 minutes when Lubomir Michalik tucked the ball home from eight yards after Chelsea failed to clear a left-sided free-kick by Idan Tal.
But their lead lasted just three minutes when Wayne Bridge raced down the left side and sent over the inch-perfect cross for Kalou to glance a low header past the Jussi Jaaskelainen from ten yards out.
Jaaskelainen was forced to stop a potential own goal from Ricardo Gardner on 24 minutes with a deft diving save from his own full-back who sliced a clearance towards goal.
Shevchenko had a half-chance two minutes later but his turn and shot was inches wide of goal.
Lampard replaced Ricardo Carvalho on 29 minutes, who injured a tendon in his left knee and the Portugal defender must now be a doubt for Liverpool.
Lampard's first touch on 30 minutes was a fantastic volley from a Bridge cross which Jaaskelainen tipped brilliantly over the bar.
Jaaskelainen was finally beaten again three minutes later and it was his own goal.
Lampard arrowed over a corner which was met at the far post by Kalou. The ball hit Tal and then the crossbar before bouncing in off the leg of the hapless keeper to put the champions into the lead.
Drogba replaced Shevchenko at half-time but it was Bolton who struck.
A short free-kick on 54 minutes left Kevin Davies free six yards out and he headed the ball past Petr Cech.
Chelsea were desperate for all three points and brought on Joe Cole for Lassana Diarra on 60 minutes.
On 73 minutes Andranik Teimourian let fly from 25 yards and the ball skimmed Chelsea's crossbar with Cech beaten.
Chelsea pushed defender John Terry upfront in a last gasp attempt to secure the win, but Bolton comfortably held on and the title looks to be heading to Manchester.