Latics eased thier way into the semi-finals for the first time ever thanks to a brace from Jason Roberts.
This was Wigan's first ever chance to progress to the semi-finals of a major cup competition, and manager Paul Jewell only made modest changes to the starting line-up compared with earlier rounds of the Carling Cup.
Ryan Taylor, Damien Francis, Alan Mahon and Andreas Johansson were all given the green light replacing Pascal Chimbonda, Gary Teale, Jimmy Bullard and Henri Camara.
The visitors imposed the physical side of their game early on but chances were hard to come by, at least until the thirteenth minute when Latics were desperately trying to clear a Stelios corner.
Abdoulaye Faye managed to get a foot on the loose ball and direct it towards the near post, but Taylor made a magnificent block from close range to deny Wanderers taking an early lead.
In the 16th minute Stelios danced his way through the Latics defence before laying the ball off to Gary Speed, but the veteran midfielders shot was straight at Pollitt.
But there was controversy straight at the other end of the pitch when Lee McCulloch and Ben Haim clashed in the penalty area. Latics pleaded for the penalty but referee Dean signalled play on.
Neither side were getting any closer to breaking the deadlock, and in the 33rd minute Damien Francis tried his luck with a thirty yard drive, but the ball flew steadily over the bar.
Thankfully Latics did score five minutes before the end of the first half, in what was their first shot on target. In a superb passing movement between Alan Mahon and Andreas Johansson, the Swede squared the ball to ROBERTS, who took a step before drilling the ball low and hard from ten yards past Jussi Jasskelainen.
Jason Roberts then doubled the lead just minutes later. Alan Mahon took advantage of a dozy Ricardo Gardner who failed to read Kevin Davies' cross. The Irish winger nipped in and carried the ball all the way down the field before releasing the ball to ROBERTS, who easily went past his marker Jaidi and dispatched the ball into the net, in almost the same way as he did for the first goal.
Half-Time: Latics 2 - 0 Bolton Wanderers
Bolton came out to try and get an instant goal from the moment the whistle was blown to signal the start of the second period. Kevin Davies laid the ball off to Speed, whose shot was blocked by De Zeeuw for corner. Then Radhi Jahdi headed just over the bar from Stelios' cross.
Wanderers should have got back in the game in the 51st minute, were it not for Stelio's shot going wide from Hidetoshi Nakata's free kick.
But with a two goal cushion, Latics were able to express themselves more freely. Jackson's long ball was headed on by Taylor to McCulloch. The Scottish international flicked the ball back to Taylor with his first touch before the former Tranmere winger curled a shot wide of the far post from twenty yards.
Sam Allardyce was getting more desperate for a goal and this prompted him to change the shape of his team to contain three strikers, with Vaz Te and Diouf replacing Stelios and Nakata.
Mike Pollitt made a remarkable save in the 66th minute when Vaz Te's shot at the near post from Diouf's corner looked certain to go in, but the former Rotherham goalkeeper smothered it.
Five minutes later, Lee McCulloch's pass through the middle of Bolton's defence sent Damien Francis on his way with a clear opportunity, but saw his shot loop off the oncoming Jaskkelainen.
The clock was ticking, and despite Wigan controlling the second half, Wanderers forced another save from the in-form Pollitt again in the 79th minute. Jay-Jay Okocha's deep cross found Vaz Te at the far post, who headed towards the target, but Pollitt tipped the ball over for a corner.
But Latics resisted everything Bolton threw at them, and even though the referee added four minutes of injury time, nothing was going to stop the party atmosphere inside the JJB Stadium. Latics are now in the hat for the semi-final draw and can almost smell the Millennium Stadium.
Full-Time: Latics 2 - 0 Bolton Wanderers
Latics Starting Line-Up: Pollitt, Taylor (Chimbonda 86), Baines, De Zeeuw (c), Jackson, Kavanagh, Francis, Roberts, Mahon (Teale 69), McCulloch, Johansson (Camara 69).
Unused Substitutes: Filan, Connolly.
Bolton Wanderers Starting Line-Up: Jaaskelainen, Nolan, Speed, Giannakopolas (Vaz Te 57), Gardner, Nakata (Diouf 62), Jaidi, O'Brien, Faye (Okocha 71), Davies, Ben Haim.
Unused Substitutes: Walker, Hunt.
Referee: M. Dean (Wirral)
