Potters striker Jon Walters equalised from the penalty spot 13 minutes from time, and Bolton's agony was only deepened by the knowledge Manchester City's dramatic late victory over QPR meant a win here would have been enough.
It looked like things were going Bolton's way at the end of the first half when Mark Davies and Kevin Davies both scored fortuitous goals after Walters had given Stoke the lead in controversial circumstances, but it was not to be.
Stoke's record on the final day of the season since their promotion to the Premier League in 2008 read played three, lost three, including the 1-0 defeat 12 months ago that helped Wigan stay up, but they began with purpose today.
Bolton looked nervy at the back, and in the sixth minute Ricardo Fuller, who could be playing his last game for the Potters, twisted and turned on the edge of the penalty area before firing in a shot that Adam Bogdan pushed round his near post.
Peter Crouch then fired wide from a tight angle while Matthew Etherington had a shot saved by Bogdan, and the Hungarian keeper was at the centre of the drama when Stoke opened the scoring in highly controversial fashion in the 13th minute.
Etherington crossed for Walters, who appeared to have taken too heavy a touch in front of goal, but the striker then headed the ball into the net seemingly out of Bogdan's hands and referee Chris Foy awarded the goal.
Stoke were causing Bolton all sorts of problems and Walters might have made it two when he turned neatly on the penalty spot but he curled his shot wide of the post.
The visitors had offered little going forward but they came within inches of scoring twice in the 32nd minute, first when Kevin Davies hit the bar with a looping header before Ivan Klasnic followed up with a sweet volley that Thomas Sorensen somehow tipped round the post.
Bolton's frustration showed when Sam Ricketts lunged into a tackle on Dean Whitehead, the full-back perhaps slightly fortunate only to be given a yellow card.
But that was nothing compared to the lucky break Bolton enjoyed in the 40th minute to provide them with a priceless equaliser.
A long ball from Bogdan was not well dealt with and Klasnic played in Mark Davies. The ball looked to have got away from the midfielder but Robert Huth smashed his attempted clearance against Davies' legs and it flew into the net.
It was reminiscent of the own goal West Brom scored that gave Bolton the lead last week, and remarkably five minutes later they were ahead, again in unusual circumstances.
Kevin Davies mis-hit his cross from the right but Sorensen was badly caught out and could only help the ball into the net at his near post.
Bolton's defensive frailties surfaced again at the start of the second half as three Stoke defenders found themselves free at the far post when Etherington curled in a free-kick, but Ryan Shawcross got his header all wrong.
Martin Petrov then came within inches of giving Bolton breathing space when he was played in by Mark Davies, the winger's shot beating Sorensen but drifting just past the post.
Ricardo Fuller was given a standing ovation as he was replaced by Cameron Jerome, who was into the action straight away as he wriggled free in the area before seeing his shot superbly blocked by Tim Ream.
Stoke were certainly not giving up and Etherington was the next player to come close to an equaliser but he was stretching as he shot and could not keep his effort down.
News from the Etihad Stadium, where QPR led City, had understandably subdued the Bolton fans, and events on the pitch had also gone somewhat quiet, although Petrov sent a 30-yard free-kick just wide.
But Bolton's hopes suffered another huge blow in the 77th minute when their side conceded a penalty, Bogdan felling Peter Crouch having initially done brilliantly to save the England man's shot, and Walters made no mistake from the spot.
Two substitutes combined for Bolton as Marvin Sordell crossed for Lee Chung-yong but he sliced his volley behind, while the Trotters were then saved by an offside flag at the other end when Crouch's effort was turned in by Jerome.
Bolton piled forward in a desperate attempt to find another goal, and Ream came close with a header from Petrov's corner that was gratefully grasped by Sorensen, but in the end there was no way back.