Ljungberg came on as a 78th minute substitute and broke Wanderers' hearts with a sweet left-foot finished in an action-packed game that saw the Gunners miss two penalties, Emmanuel Adebayor score twice and Bolton's Tal Ben-Haim sent off.
Make no mistake about it, Arsene Wenger will have been furious with his troops for letting the game slip through their fingers at the last.
They had been in complete control of this fourth round replay for the majority of this tie and looked to be going through until deep into injury-time.
But their lack of conviction and shoddy finishing meant that they were taken into extra-time by Abdoulaye Meite's 91st minute equaliser.
The worst of which came four minutes from the end of normal time when Adebayor hit the post after skipping round Jussi Jaaskelainen in goal.
In all fairness to the Gunners striker, he had very strong competition for that gong from skipper Gilberto Silva who blazed a 64th minute penalty over the bar.
Brazil striker Julio Baptista also had a couple of chances to extend Arsenal's lead but poked wide a Tomas Rosicky cross and also saw a free-kick tipped over.
Arsenal despise trips to the Reebok - they have lost four times here in recent seasons - and you just got the feeling that they were hating this trip the longer it went on too.
Bolton's method for hurting Arsenal is to hustle and bustle their opponents into submission, and once Gilberto had missed from the spot, the fight back was on.
Nicolas Anelka and El Hadji Diouf used their skill and pace to worry the Gunners defence, before Diouf delivered a telling left-wing corner at the death that Ivan Campo got his head to and Meite did the rest.
But then came Ljungberg's extra-time strike which he finished after a neat lay-off from fellow sub Jeremie Aliadiere.
Adebayor's tap-in and second of the game made things completely safe after Baptista had missed from the spot.
Ben Haim had been sent off for his second bookable offence just a few minutes before the penalty.
The men from the Emirates now face a fifth round home tie against Blackburn Rovers on Saturday after only their second victory against Bolton in nine league and cup meetings.