Danny Welbeck was the beneficiary of a dubious penalty but helped finish off AC Milan after Granit Xhaka's insurance strike in the second leg of their last-16 clash.
Arsenal reached the Europa League quarter finals on Thursday with an assured performance to see off AC Milan at the Emirates Stadium.
Arsene Wenger's side welcomed AC Milan to north London with high hopes of advancing to the quarter finals of the competition. Wenger's side were successful in the reverse fixture at San Siro, hitting two away goals past the Italians in what ended up a fairly convincing result.
Arsenal made two changes to the their first leg starting lineup with Nacho Monreal and Héctor Bellerín coming in for Sead Kolašinac and Calum Chambers.
Gennaro Gattuso also made a few changes - switching to a 4-4-2 formation from a more attacking 4-3-3 with Fabio Borini and André Silva coming in for Davide Calabria and Giacomo Bonaventura.
The hosts were dealt an early blow around the 10 minute mark when captain Laurent Koscielny went down with what looked like a back injury. Calum Chambers leapt to the touchline as the Frenchmen passed his arm band to Jack Wilshere and the game resumed with an altered Arsenal back line.
As the first half reached its midway point the deadlock remained despite a sudden burst of end to end football which saw Danny Welbeck pick up the best chance of the opening stages - receiving the ball deep down Milan's right, though the England striker was unable to beat the goalkeeper at the near post.
Hakan Çalhanoğlu sent a torrent of panic through the Emirates stadium with a thunderbolt of a strike from more than 25-yards out, beating an outstretched David Ospina. Granit Xhaka had failed to get close to his man and Arsenal were punished through his mistake.
Only seconds later the drama continued - Welbeck went down in the box after what looked like the slightest of touches from Ricardo Rodríguez' hand. However, the referee thought otherwise and Welbeck obliged with a cool finish into the bottom left corner, restoring Arsenal's two goal lead.
Aaron Ramsey should have made it 2-1 when the Welshman was played in through a delicate lay-off from Mesut Özil, himself doing well to get in a great position just outside the box. Ramsey couldn't make the most of his effort, however, which ended up yards wide of the crossbar, to the relief of the away support.
AC Milan substitute, Nikola Kalinić, looked like getting his team a second with his first touch after Leonardo Bonucci played in an excellent long cross, pinpointed to the Croatian's position in the box; the striker should have done much better, providing a timid shot that Ospina could have saved in his sleep.
Kalinić's miss proved all the more pivotal as moments later Xhaka looked to send his team into the quarter finals with a great strike from outside the Milan box. Gianluigi Donnarumma should have done much better between the sticks, only managing to divert the ball into the net with his half-hearted attempt at a save - AC Milan now needing three goals in less than 15 minutes at 4-1 on aggregate.
Welbeck got his second on the night, making it 3-1 as the game approached the 90-minute mark. Jack Wishere moved the ball nicely down the left, dinking a delayed cross onto the head of Ramsey who was unable to beat the keeper. Welbeck was the first to react as Arsenal had surprisingly piled men forward despite such a lead, heading the rebounded save into the back of the net.
AC Milan gave their all but unfortunately the Gunners were too good over the course of two legs and now look forward to the Europa League quarterfinal draw.