Stoke set the Trotters on the road to Championship football after 13 minutes when Jonathan Walters bundled both Bolton goalkeeper Adam Bogdan and the ball he was holding into the net.
But Bolton hit back to take the lead before half-time, Mark Davies equalising with a high-speed deflection off his groin and Kevin Davies then finding the top corner from an acute angle while 35 yards out on the right flank.
Bolton could not hold on to win, however, with Walters scoring from the spot after Peter Crouch was brought down in the box under the lightest of challenges from Bogdan.
That was how the match finished, and despite QPR being beaten by newly-crowned champions Manchester City, Owen Coyle's were sent out of the top flight.
Both sides came into the match on the back of terrible runs of form, with Bolton having won just one of their last eight and Stoke one of their last 10 matches in the league.
But it was Stoke who seemed determined to end the season on a high, taking the game to Bolton from the start and peppering Bogdan with shots at goal.
Ricardo Fuller, Crouch and Matthew Etherington all had good chances within the first dozen minutes, but when the breakthrough came it was courtesy of perhaps the worst refereeing injustice of the season.
Etherington's cross from the right picked out Walters, who beat the offside trap and chested the ball into the path of Bogdan. The Trotters' keeper had both hands firmly on it, but Walters's momentum saw him bundle straight into the keeper, sending both Bogdan and the ball flying into the net.
The Stoke midfielder barely knew a thing about it as he spun round to stay on his feet while everyone in the stadium waited for Chris Foy to blow up for a foul. The whistle only came to signal a goal, however, and Stoke took a justified lead with an unjustifiable decision.
Bolton were sparked into action, with Davies hitting the bar with a header and Thomas Sorensen pulling off a miraculous diving save from Ivan Klasnic's drive.
But given the circumstances of the opening goal it was probably fitting that it came in bizarre circumstances as a wild 39th-minute clearance by Robert Huth clattered Mark Davies in the groin, with the ball ricocheting at stunning speed into the Stoke net.
And just before half-time Bolton made it 2-1 with another odd goal, Kevin Davies's effort from the right touchline flying straight in at the top corner by the near post. If he meant to do it, it was a goal of the season effort - but the veteran will no doubt admit that it was luck rather than judgement which saw him beat the Stoke goalkeeper.
With Manchester City winning against QPR, Bolton came out after half-time seemingly more determined to stay ahead than add an extra cushion to their lead, and the home side quickly established control of the match.
Despite that it was Petrov who nearly scored the next, with a first-time shot that swerved inches past the right upright six minutes after the break.
That goal would have been against the run of play though, with Bolton putting seven or eight men behind the ball, and when Etherington missed on the hour mark it seemed that the game would be destined to finish 2-1.
Yet an equaliser came, once again in controversial circumstances as Crouch went down in the box under a feather touch from Bogdan and Foy pointed to the spot.
Walters converted the spot-kick with a thumping effort. However with news of QPR's unlikely 2-1 lead at Manchester City filtering through, it seemed that the result would nonetheless be moot.
A disallowed offside goal from sub Cameron Jerome and Sorensen's brilliant save from Tim Ream's injury-time header could have seen either team snatch the points, but the match ended in a draw which sent Bolton into the Championship.
Worse heartbreak was to come for Bolton, however, as the news of two injury-time goals at Eastlands left them in the knowledge that a win would have kept them safe.