The Gabonese striker missed from the spot in the final minute of the north London derby a week ago, but found the net here to seal a 2-0 win at the Emirates after Granit Xhaka had opened the scoring.
The victory, which ended Ole Gunnar Solskjaer‘s 100% away record, sends Arsenal into fourth spot, just a point behind rivals Tottenham, having completed all of their fixtures against the other top six sides.
Unai Emery made five changes to the side that lost in Rennes, selecting all four of Aaron Ramsey, Mesut Ozil, Alexandre Lacazette and Aubameyang in an attacking line-up, while Ainsley Maitland-Niles came in at right wing back.
The visitors had Nemanja Matic back from injury alongside Paul Pogba, who missed the heroic win in Paris through suspension.
First it was Chelsea, beaten 2-0 here in January and subsequently relegated to sixth place, now Manchester United, defeated by domestic opponents for the first time in Ole Gunnar Solskjaer’s tenure and edged out of the Champions League top four.
Arsenal face Rennes on Thursday in a competition that has come to be known as their Champions League safety blanket. If it stays like this, however, it is Solskjaer who will need to land the big one to be it in next season. Curtis Mayfield’s ‘Move On Up’ serenaded the fans as they walked into the night and the rain – and Arsenal have. They lead Manchester United by two points and trail Tottenham by one.
Pierre-Emerick Aubameyang put the finishing touches on Arsenal’s 2-0 win over Manchester United at the Emirates Stadium
Granit Xhaka attempted a speculative strike from range early on and it wrong-footed United keeper David De Gea
Manchester United players look perplexed that the seemingly benign effort found its way past the Spanish stopper
Pierre-Emerick Aubameyang then stepped up calmly to slot home a penalty after Fred brought down Alexandre Lacazette
The Gunners striker leaps and punches the air after sealing all three points for Unai Emery’s side at the Emirates Stadium
A supporter ran across the pitch and confronted Chris Smalling after the second goal – police later made an arrest