The hero was Mark Davies, who would not have been in the side had it not been for Stuart Holden's thigh injury, who fired home in the 89th minute to round off a glorious team move and snatch what seemed an unlikely result with 15 minutes remaining.
Thumping: Blackpool's Ian Evatt (right) scores the opening goal
Substitute Martin Petrov had pulled one back for Wanderers in the 76th minute.
Blackpool looked set for a fourth victory in nine away matches after headers from Ian Evatt and Luke Varney as the Seasiders but the team with the worst defensive record in the Barclays Premier League could not hang on under intense late pressure.
Bolton, who remain in fifth place as a result, extended their unbeaten run to five matches but made hard work of it at times as they had plenty of chances to score both before and after the visitors went ahead.
Matt Taylor tried to mark his 29th birthday and 350th league appearance with an early goal but his second-minute free-kick was comfortably saved by Richard Kingson.
It sparked a spell of sustained Wanderers pressure which should have brought the opening goal but failed to.
Luke here: Varney (right)celebrates after scoring Bolton's second goal
Surprisingly captain Kevin Davies made the wrong choice in opting to shoot near-post instead of across Kingson after being put through the inside-right channel by Johan Elmander and earned only a corner.
Taylor's dipping volley from Gary Cahill's knockdown landed on the roof of the net while Lee Chung-yong had his 10-yard shot blocked by a combination of Stephen Crainey and Evatt.
But having dominated the opening 27 minutes Bolton succumbed to a familiar failing.
Owen Coyle's side have not kept a clean sheet since the opening day of the season and they were unable to end that run on this occasion.
The Seasiders had been restricted to the odd counter-attack but, unlike their opponents, they took full advantage when a chance presented itself just before the half-hour.
DJ Campbell's shot took a double deflection off Cahill and Zat Knight only to bounce wide with Jussi Jaaskelainen wrong-footed.
Late show Mark Davies scores the equaliser for Bolton
However, the goalkeeper should possibly have done better from Evatt's flick-on from the resulting corner but the Finland international could only finger-tip the ball inside the far post.
Taylor-Fletcher could have made it 2-0 almost immediately but he ballooned over a cut-back from Charlie Adam who, in an example of how Blackpool's confidence had risen, attempted an ambitious 50-yard effort from just inside Wanderers' half which only just cleared the crossbar.
The second half began with Lee shooting weakly at Kingson when well placed and Kevin Davies being crowded out by Neal Eardley as he tried to reach Taylor's far-post cross.
But as had happened before the break Blackpool were the ones who took their chance when it came in the 58th minute, and again it came from a left-wing corner.
Grandin's inswinger was met by the head of Varney and Taylor-Fletcher cleverly ducked out of the way to allow the ball to continue its path to goal despite the best efforts of Lee on the line to keep it out.
Coyle made an immediate double substitution, sending on Petrov and Rodrigo Moreno for Taylor and Lee.
The visitors were fortunate Kingson's half-stop from Elmander's narrow-angle shot bounced the wrong side of Kevin Davies in the six-yard area but they were soon on the attack again, with Jaaskelainen sticking out a leg to deflect Campbell's effort wide.
Campbell's pace was proving a real danger on the break and the striker poked the ball just wide of the far post having found space on the right of the penalty area.
But Petrov gave his side hope 14 minutes from time with a smart individual effort, flicking up Mark Davies' pass with his right foot and smashing home from the edge of the area with his left.
They should have had an equaliser when Kingson palmed Mark Davies' header out to namesake Kevin but he could only stab wide from five yards.
In a grandstand finish Petrov had a close-range volley cleared off the line by Crainey before an intricate move carved out a second a minute from time.
Started and finished by Mark Davies, it involved a neat string of passes between Kevin Davies, Elmander and substitute Ivan Klasnic before the midfielder ran in to smash home from close range.
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