Following the aggregate loss to Bayern Munich in the Champions League, the Gunners came to Bolton in a bid to keep their last hopes of winning a trophy alive this season in this sixth round tie.
Bolton who had lost only once in the last 12 outings were without skipper Jay Jay Okocha, injured in the 1-0 Premier League win at Manchester City last Monday.
Gary Speed returned in place of Okocha and Nicky Hunt was back at right-back after recovering from a dislocated shoulder. Vincent Candela was relegated to the subs bench.
Arsenal were without several stars included Sol Campbell, Edu and Thierry Henry who was injured in midweek.
Bolton were trying to repeat their Premiership form against the Gunners after recording a 2-2 draw at Highbury and a 1-0 win at the Reebok this season.
Arsenal drew first blood, hitting the target in only the third minute. A Hunt slip let in Robert Pires, whose throughball found the unmarked Ljungberg who chipped the ball over by the advancing Jussi Jaaskelainen and into the net just inside the far post.
Worse was to follow for Bolton who had striker El Hadji Diouf sent off in the ninth minute after appearing to strike Arsenal keeper Jens Lehmann, who fell to the ground clutching his face.
Bolton tried to re-group and embarked on the spell of pressure. Lehmann saved a Kevin Nolan shot and minutes later Lauren was there to save again when Stelios Giannakopoulos got in a header at goal.
Lehmann had a stroke of luck when a Bruno N'Gotty free-kick bounced just in front of him and skidded, hitting him on the shin before he gathered the ball.
Then it was Arsenal's turn to attack and Jaaskelainen saved with his feet when Dennis Bergkamp sent Jose Antonio Reyes through and he tried to slide the ball past the keeper.
Giannakopoulos could get no power behind a header at the Arsenal goal, then Jaaskelainen was brought back into action, saving a long-range shot from Bergkamp.
The Bolton keeper saved at the second attempt when Ljungberg powered in a shot at goal and was then on hand to make a fine diving save when a Reyes shot looked set to creep just inside the post.
A foul on Kevin Davies brought Bolton a free-kick midway inside the Arsenal half. N'Gotty played the free-kick into the goalmouth where the ball eluded everyone and Lehmann looked relieved to see it drift past the upright.
A spell of Bolton pressure ended when Arsenal broke quickly and Bergkamp sent Reyes away to fire in a shot which brought a fine diving save from Jaaskelainen.
Bergkamp brought another excellent save from Jaaskelainen when he fired in a free-kick from just inside the penalty area that the Bolton keeper tipped over the bar.
Bolton's Giannakopoulos headed inches over the ball in the dying moments, but Arsenal had few problems holding their lead and Ljungberg even missed an absolute sitter in the last minute of stoppage time.
Man of the Match: Jussi Jaaskelainen - The Bolton keeper had no chance with the Arsenal goal, but made a series of super saves to prevent the Gunners from adding to their tally.