For Sheffield Wednesday in the fourth round, read Wimbledon in the quarter-finals.
Bolton, one of English football's leading giant-killers of the 1990s, claimed a second Premiership scalp in a fortnight last night to move into the semi-finals of the League Cup.
Eidur Gudjohnsen, with a superb solo effort, and a Michael Johansen penalty gave the Division One side victory after Carl Cort had put Wimbledon in front.
It means Wanderers are just 180 minutes away from a second appearance in the final in six seasons after they were runners-up in 1995.
Bolton will meet Tranmere in the last four after they beat Middlesbrough last evening, ensuring a Nationwide League team will make it all the way to Wembley.
Bolton made hard work of it, though, coming from behind after the visitors had dominated the opening half-hour.
They then had to withstand a constant barrage of pressure after the interval as Egil Olsen's men looked for an equaliser.
Cort gave Wimbledon the lead in the 17th minute, slotting home his 11th goal of the season after John Hartson had prised open the Bolton defence.
Cort went on to hit the post but Wanderers stunned the Premiership side with two goals in six minutes.
First Gudjohnsen, for whom Derby had a £4 million bid rejected earlier this month, scored a terrific goal. The Icelander went past four defenders before beating Neil Sullivan from eight yards.
That 33rd-minute strike gave Bolton confidence, and Gudjohnsen should have put them in front shortly afterwards.
Wimbledon failed to clear Johansen's near-post cross and Bob Taylor was able to help the ball back to the 21-year-old.
He was only 10 yards out, but somehow the striker missed.
However, Bolton did not have long to wait to go in front. Ricardo Gardner swung over a corner from the Wanderers right and Taylor clearly had his shirt tugged as he tried to challenge for the ball.
Referee Alan Wilkie immediately pointed to the spot and Johansen made no mistake.
Bolton Wanderers: Jaaskelainen, Holden, Fish, Bergsson, Whitlow, Johansen, Jensen, Elliott, Gardner (Aljofree 88), Taylor (Strong 81), Gudjohnsen (Hansen 86). Subs Not Used: Banks, Passi. Booked: Elliott, Gudjohnsen, Whitlow. Goals: Gudjohnsen 34, Johansen 39 pen.
Wimbledon: Sullivan, Ardley (Leaburn 71), Cunningham, Andersen, Kimble, Earle, Roberts, Euell, Gayle, Hartson, Cort. Subs Not Used: Davis, Hughes, Waehler, Badir. Booked: Roberts. Goal: Cort 17.
Referee: A Wilkie (Chester Le Street).