Comeback kings City looked to have salvaged a point when Rory Delap ended a 21-month goal drought in the 48th minute to cancel out Lee Chung-yong's opener midway through the first half.
But from Gretar Steinsson's deep throw into the area in the second minute of injury time, 77th-minute substitute Ivan Klasnic fired home the winner.
Klasnic, though, went from hero to villain moments later as he was dismissed for two bookable offences in a matter of minutes after his goal.
It was a chaotic, turbulent finish to a game that also saw rival fans clash in one corner of the Reebok Stadium before police and stewards intervened.
Prior to that, and for two of the top flight's lesser lights, it was an entertaining affair.
From both teams, up until the rashness of the final minutes, there was a desire to play football, to search for an opening rather than pump aimless long balls forward in the hope of catching a break.
Ahead of Lee's opener, Stoke looked a side on the rise after a run of three wins and a draw from their previous four league matches.
Their play exuded the greater degree of confidence, and arguably they should have taken a 15th-minute lead from an inswinging corner by Matthew Etherington.
But despite piercing Bolton's six-yard box, neither Robert Huth nor Abdoulaye Faye were able to apply the finishing touch required at the far post.
Three minutes later, as a gap opened up in Bolton's defence, winger Etherington was left smacking his forehead in disgust with himself as a low 18-yard shot lacked power and was safely gathered by Jussi Jaaskelainen, who should have been more severely tested.
As the midway point of the half approached Bolton had conjured little in response, so it is fair to say Lee's strike came out of the blue.
After playing a one-two with skipper Kevin Davies, Lee was lucky to see a follow-up attempted pass ricochet off Faye into his path.
The Korean needed no second invitation as he quickly pounced on the loose ball to stab a first-time effort past Sorensen from 19 yards.
Not for the first time this season it left Stoke being asked to come from behind, and they were almost level just after the half-hour only for Jermaine Pennant's dipping 25-yard free-kick to strike the top of the crossbar.
At that stage, with chances flowing at both ends, Fabrice Muamba should have made it 2-0, only for his first-time drive to narrowly clear the bar after he had been teed up by Davies.
After referee Peter Walton ignored furious penalty appeals from Stoke as a loose ball had rolled over the arm of an unaware Zat Knight, Bolton again wasted the chance to increase their lead.
In injury time Thomas Sorensen initially produced a superb one-handed save in turning aside a rasping drive from Martin Petrov.
From the ensuing corner to the far post, Davies missed a sitter as he steered a header wide when the ball should have been nestling in the bottom corner of the net.
It proved costly because within three minutes of the restart Stoke were level. From Etherington's corner, Huth's knockdown arrived at the feet of Delap who volleyed home from five yards.
Just before the hour Stoke almost completed another comeback as Kenwyne Jones and Jon Walters combined to set up Dean Whitehead for a first-time effort which Jaaskelainen saved with his legs.
Wanderers, though, were far from out of the picture as Davies was again the supplier shortly afterwards with a flick-on from a long ball for Johan Elmander, whose steered effort through the six-yard box was inches beyond the far post.
After a looping Danny Collins header from a deep Pennant cross also failed to fall inside the far post moments later, the game appeared set to peter out.
But a rash of substitutions, including Klasnic, proved pivotal for Bolton as the striker pounced to steal the points and end a run of three successive home draws, only to blot his copybook with his red card after an altercation with Whitehead and a foul on Huth.