Second Division Tranmere Rovers produced a late knockout to flatten Wanderers' FA Cup hopes.
Iain Hume decided the tie in the opening seconds of extra time when he thundered a 25-yard piledriver into the net.
A minute earlier Bolton looked as if they had saved the tie, Ricky Shakes firing in an injury-time equaliser after Eugene Dadi had given Rovers an 82nd minute lead.
Yet as Tranmere contemplated a fourth round trip to Luton, Wanderers boss Sam Allardyce was left to concentrate on his two main priorities.
He admitted before the game that Premiership survival and a Carling Cup semi-final against Aston Villa were his main concerns - a point proved by making ten changes from the side that beat Blackburn on Saturday.
The game probably saw the end of Mario Jardel's brief excursion into English football.
The former Golden Boot winner was substituted at half time fuelling speculation that Bolton were ready to end a short stay that never saw the Brazilian start a Premiership game.
Danish striker Henrik Pedersen could have gone some way to settling the tie with his first and last touches of the first half.
Inside the first minute he found himself inside the six-yard box but could not control the ball to test John Achterberg in the Tranmere goal.
He tested the Tranmere defence on the stroke of half-time, however, firing a free-kick from just outside the area and striking the post only to see the ball rebound clear.
In between, both sides shared equal chances but provided little threat.
Tranmere's best chance came at the far post, where Danny Harrison just failed to hook the ball in from an acute angle while Portuguese teenager Ricardo Vaz Te went close for Bolton.
Jardel never got to grips with the first-half action. His solitary contribution was winning the dubious free-kick from which Pedersen hit the woodwork.
Kevin Nolan replaced the Brazilian after the break, but it was Tranmere who looked the more dangerous.
Kevin Poole, the hero for Wanderers in the first meeting at Prenton Park, foiled Rovers again with a good stop from David Beresford and then after Jeff Smith had been caught out in his own area, Ryan Taylor blazed a good chance high over the bar.
Bolton's response was a nicely worked move that ended with Vaz Te giving Nolan a clear sight of goal only for the midfielder to fire narrowly wide.
Yet when Dadi fired Rovers ahead in the 82nd minute it only served to set up a late thriller, with Shakes equalising with a shot that deflected in off Graham Allen before Hume finally settled matters.