Taylor's goal ensured Bolton ended the season with a draw
Bolton's Matthew Taylor scored a late equaliser but with Manchester United winning at Wigan the goal did not cost Chelsea the Premier League title.
To add to Chelsea's disappointment, skipper John Terry dislocated his elbow but he is hopeful of being fit for the Champions League final on 21 May.
Ali Al Habsi denied Florent Malouda and Didier Drogba before substitute Andriy Shevchenko struck from six yards.
Ashley Cole cleared off the line before Taylor struck with a low drive.
Central defender Alex was culpable for the equaliser after a sloppy, lazy clearance that fell invitingly to Taylor.
But in truth, there can be little doubt that the players already knew that with United leading 2-0 at Wigan their valiant quest to wrestle the title from Sir Alex Ferguson's team was going to fall short.
Grant hails Chelsea's title challenge
A win would have at least ensured that Chelsea finished the season with the same number of points as United, losing the title on goal difference.
But Avram Grant's team, who in drawing with Bolton stretched their unbeaten run in the Premier League to 21 games, will have the chance to ensure their season does not end trophyless when they meet United in the Champions League final in Moscow.
Whether skipper Terry is able to play any part in that contest remains to be seen after his 11th-minute injury.
Chelsea had already created one good chance - Drogba failing to divert Michael Ballack's low cross into the goal - when they lost Terry.
Petr Cech, Terry and Kevin Davies competed for a long ball upfield, with the Chelsea goalkeeper leaping high off the ground to make an authoritative claim.
However, Cech appeared to catch Terry with his knee and the Chelsea skipper tumbled to earth.
The defender, clearly in a great deal of pain, was stretchered from the field with his left arm in a makeshift sling fashioned from his shirt.
Undaunted by the loss of Terry, Chelsea continued to dominate possession, while Bolton worked hard to maintain their shape and close the opposition down quickly, limiting clear-cut openings.
Drogba was inches wide with a free-kick, while Gretor Steinsson made a brave challenge after the ball almost broke to the Ivorian six yards from goal but Bolton reached the break on level terms in relative comfort.
The Bolton players made their Chelsea counterparts wait for several minutes before reappearing for the second half but if the tactic was supposed to unsettle Grant's team, it did not work.
Within minutes of the restart, Al Habsi made a brilliant fingertip save to deflect Malouda's looping strike on to the crossbar, while a last-gasp block denied Juliano Belletti.
Megson pleased with battling Bolton
Al Habsi made another superb save, this time tipping over a strike from Drogba after a rampaging burst forward before substitute Shevchenko finally ended Bolton's stubborn resistance.
A mis-hit strike from the edge of the box eluded numerous bodies before running to Shevchenko, who made a poor contact from six yards but nonetheless found the net.
Bolton showed more ambition after conceding and finally started to create some chances.
Cech smothered a close-range shot from El Hadji Diouf, while Gavin McCann saw a looping header rebound off the crossbar before Ashley Cole cleared the danger.
And in the third minute of injury time Bolton scored the goal that ensured their Premier League survival was not merely on goal difference after Alex's poor clearance.
Chelsea: Cech, Essien, Alex, Terry (Belletti 14), Ashley Cole, Ballack, Makelele (Shevchenko 46), Lampard, Joe Cole (Obi 78), Drogba, Malouda. Subs Not Used: Cudicini, Kalou.
Goals: Shevchenko 62.
Bolton: Al Habsi, Steinsson, Andrew O'Brien, Cahill, Samuel, Davies, Joey O'Brien, McCann, Nolan, Taylor, Diouf (Giannakopoulos 69). Subs Not Used: Walker, Jaaskelainen, Meite, Cohen.
Booked: Joey O'Brien, McCann, Davies.
Goals: Taylor 90.
Ref: Chris Foy (Merseyside).
BBC Sport Player Rater man of the match: Chelsea's Didier Drogba 7.18 (on 90 minutes).
Please note that you can still give the players marks out of 10 on BBC Sport's Player Rater after the match has finished.
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