A huge upset looked to be on the cards heading into the final minute of time, before Kieran Gibbs and substitute Lukas Podolski scored within two minutes of each other to rescue a valuable win for the Gunners.
Here, Sports Mole takes an in-depth look at how the action unfolded at the Constant Vanden Stock Stadium.
On target: 3
On target: 4
Was the result fair?
With just one minute of normal time remaining at the Constant Vanden Stock Stadium, Arsenal were trailing 1-0 and looked completely devoid of any ideas. Anderlecht squandered a couple of chances to double their advantage, and the game was seemingly up as home supporters began to celebrate one of the great results in their club's history.
Credit must go to the Gunners in the end for digging themselves out of an ever-deepening hole, thanks to strikes from Gibbs and Podolski in the dying embers of the game. There was just one minute and 45 seconds between the two goals which helped not just rescue a draw, but salvage all three points at the death for the visitors.
Arsenal were not at the races at all this evening, and although Besnik Hasi's charges were hardly sensational themselves, they were good value for their lead when it eventually came on 71 minutes. As it was, though, Anderlecht just could not hold out, and the top two places in Group D look to have been wrapped up with three games left to play.
The Purple and Whites do not exactly boast the best of records against English opposition, having gone seven games and 14 years without a win over a Premier League side. In fact, Anderlecht's Champions League record in general has been terrible in recent times, with just two victories to their name in 33 attempts.
Despite this, the Belgian Pro league champions refused to sit back this evening, which many expected to be the case following their thumping 3-0 reverse at the hands of group leaders Borussia Dortmund last time out. Hasi fielded a young and inexperienced side, keeping star striker Aleksandar Mitrovic on the bench from the start. It would be harsh to say that their lack of overall experience cost them in the end, but Anderlecht did show some naivety to throw away the game at the death.
The Gunners came into this European fixture having won just two of their eight games in the Premier League so far this season, hoping to pick up a comfortable victory in order to refocus attention on domestic matters. It was clear to see from the off that it was not going to be all that easy, however, as their opponents looked to spring attacks of their own.
Poor defending very nearly cost Arsenal dearly, and the performance of Alexis Sanchez aside, not a single player could hold their head up high prior to that late rescue mission. The North London outfit will just be pleased to have left Belgium with all three points which keeps them within touching distance of Dortmund, although in many ways it papers over some lengthening cracks. One clean sheet in 10 and a lack of creative ability when the pressure is on highlights the Gunners' frailties, which must be sorted out in due course.
Sports Mole's man of the match
Andy Najar: He looked lively throughout, but following his well-taken headed goal 20 minutes from time, Najar stepped his performance up another level to cause Arsenal real problems down the right. The midfielder also set up a brilliant chance which Anthony Vanden Borre failed to capitalise on at 1-0, which proved very costly in the end.
Not for the first time this season Arsenal looked very nervous at the back, particularly down the flanks when Anderlecht pushed up the field. The goal should have been dealt with, but worse than that came shortly after when a long ball over the top was not cleared by Per Mertesacker or Nacho Monreal, which nearly led to a second goal for the hosts. The makeshift centre-back had a torrid time, which backs up manager Arsene Wenger's recent acknowledgement that he is in need of a new defender or two in January.
Carlo Velasco did not have a great deal to do throughout, but he allowed the game to flow when he could which helped create a brilliant spectacle late on.
Anderlecht: These two sides meet again in two weeks' time, but before then the Purple and Whites take on Standard Liege in the Belgian Pro League.
Arsenal: The Gunners will be looking to turn around their poor Premier League form when they travel to face Sunderland on the weekend.