The Gunners welcomed the Red Devils to Emirates Stadium on Sunday aware of a stunning run of form being enjoyed by Ole Gunnar Solskjaer.
They were, however, to inflict a first Premier League defeat on the Norwegian as they kept a priceless clean sheet and worked two goal-scoring opportunities.
Granit Xhaka broke the deadlock inside 12 minutes with a swerving shot from distance which left David de Gea wrong-footed.
Arsenal then won a penalty in the 69th minute and Aubameyang made no mistake to wrap up the points and a win which has lifted Unai Emery’s side back into the Champions League spots.
The Gabonese striker told Sky Sports of the importance of claiming a win over a direct rival: “The spirit of the team was good.
“We have everything in our hands and we know it will be tough to finish in the top four, but we are confident - it was important to win this game today and we have chances.
“We have a good spirit and we are hungry - we want to come back into the Champions League.”
Arsenal are now just one point adrift of north London neighbours Tottenham, with it possible that third place could still be up for grabs.
The Gunners could already be sat above Spurs, but saw two points slip through their grasp on derby day at Wembley Stadium.
Aubameyang failed with a late penalty in that contest, but was successful from 12 yards against United.
He now has 17 Premier League goals to his name, putting him one behind Manchester City’s Sergio Aguero in the race for the Golden Boot, and is pleased to have got his eye back in.
“I made a mistake against Tottenham and I missed it, but today I was focused and scored a penalty,” added Aubameyang.
“You have to practice this all the time and I did. I knew it would be tough, but I was really confident.”
The international break will then delay their return to Premier League action until April 1 when they are due to play host to Newcastle.