FA Cup holders Arsenal were punished for fielding an inexperienced line-up as Bolton knocked them out of the competition at the fourth-round stage.
Giannakopoulos heads in Bolton's winner against Arsenal
Stelios Giannakopoulos grabbed the winner as he headed in a Ricardo Gardner cross late on when it seemed the game was destined for a draw.
Robin van Persie had earlier headed against the crossbar for Arsenal.
Gunners duo Freddie Ljungberg and Sol Campbell also went close with shots on goal before Bolton's winner.
Arsenal, who crashed out of the Carling Cup semi-finals on Tuesday, fielded a line-up missing Thierry Henry, Jens Lehmann, Lauren, Robert Pires, Gliberto and Francesc Fabregas.
Boss Arsene Wenger's young side had an early chance when midfielder Abou Diaby had a shot from eight yards deflected over before the home side began to take control in front of a meagre 13,326 crowd.
Bolton striker Davies is challenged by Arsenal defender Campbell
Bolton striker Jared Borghetti had a free header and fellow forward Kevin Davies had a shot at goal but each lacked the composure to apply the finishing touch.
That was a rare glimpse of goalmouth action during a disjointed first half in which both sides stifled one another.
Jose Antonio Reyes summed up the lack of quality in the match when he was found with time and space by Aleksander Hleb only to blaze a wayward shot high.
The match became more physical after the interval and Diaby was booked for a late tackle on Ivan Campo, who was forced off as a result.
Ricardo Vaz Te came on for Campo and he broke into the Arsenal box from the right wing before being caught in two minds whether to shoot or cross and seeing his effort across goal go harmlessly wide.
Van Persie headed a Freddie Ljungberg cross against the crossbar as the game finally started to pick up.
Ljungberg sent a well-struck shot just over before Campbell did the same from eight yards following a scramble in the Bolton box.
But Arsenal failed to find a way through the Bolton defence and were caught out when Giannakopoulos nodded in at the far post to repeat the Trotters' Premiership win against the Gunners earlier this season.
Bolton boss Sam Allardyce:
"I didn't think Arsenal would be quite as adventurous as they are with a full strength side. "But we wore them down and pulled out an absolutely wonderful goal to get us through to the next round. "If we come out of the hat first again in the next round that means that teams will have some trepidation coming here."
Arsenal manager Arsene Wenger:
"I feel we should have won this game by three goals difference.
"Bolton didn't create anything the whole game and won with one chance and one goal. Practically, we have lost two trophies this week in the last minute.
"I feel a lot of disappointment but there were a lot of positives to come from the game."
Bolton: Jaaskelainen, O'Brien, Ben Haim, N'Gotty, Gardner, Nolan, Campo (Vaz Te 54), Nakata, Davies, Borgetti (Jansen 73), Giannakopoulos (Hunt 89).
Subs Not Used: Walker, Fojut.
Goals: Giannakopoulos 84.
Arsenal: Almunia, Gilbert, Senderos, Campbell, Djourou, Diaby, Flamini, Hleb, Ljungberg, Van Persie, Reyes.
Subs Not Used: Poom, Larsson, Bendtner, Lupoli, Muamba.
Booked: Reyes, Diaby, Senderos, Van Persie, Gilbert.
Ref: M Dean (Wirral).