Owen Coyle's side needed a victory at the Britannia Stadium and a QPR defeat against Manchester City to climb out of the bottom three on the final day of the season.
But they were unable to complete their half of the job and a painful campaign, marred by Fabrice Muamba's cardiac arrest and serious injuries to key players, ended with the cruellest blow of all.
With QPR beaten by two late City goals, Wanderers would have survived if they had held onto a 2-1 half-time lead secured by goals from Mark Davies and Kevin Davies after Jonathan Walters put the hosts ahead.
But Walters equalised from the penalty spot 13 minutes from time and Bolton couldn't find a winner as they sunk into the Championship, finishing third bottom and one point behind QPR.
Stoke were quick to test Bolton's nerves and Ricardo Fuller 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 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.
And Bolton finally enjoyed a lucky break to equalise in the 40th minute.
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.
Remarkably five minutes later Bolton 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.
Martin Petrov came within inches of giving Bolton a crucial third goal when he was played in by Mark Davies, but the winger's shot flashed just past the post.
But Bolton's hopes suffered another huge blow in the 77th minute when Bogdan conceded a penalty by fouling Peter Crouch, having initially saved the England man's shot, and Walters made no mistake from the spot.
Bolton piled forward in a desperate attempt to beat the drop, but the closest they came was a Tim Ream header from Petrov's corner that was grasped by Sorensen.
Source: AFP
Source: AFP