The pair spent three years together at Dortmund, and reunited in January, as Mkhitaryan moved to the Emirates from Manchester United in a swap deal that saw Alexis Sanchez go the other way, while Aubameyang was recruited in a club-record £55 million deal.
The two played together for the first time since their Dortmund days against Everton, with Aubameyang netting his first goal in a 5-1 win, and Mkhitaryan providing three assists.
While the two did little to harm Tottenham in the north London derby at the weekend - the Gunners slipped to a 1-0 loss - Mkhitaryan has hailed the club's recruitment of one of his "best friends".
“We did not have too much time to train together (before the Everton game),” Mkhitaryan told the club’s website.
"He came a bit late, like two days before the game and he had been training only twice.
"I thought it could only be in a dream that we could join another club other than Dortmund but I am very happy for that.
"I know him very well, he is one of my best friends and one of the best team-mates I have ever had.
"I am very happy to have him here and I think all the fans are happy to see him in an Arsenal shirt. What can I say? I love playing with him.”
Arsene Wenger expressed his hope that the two players would provide a fresh impetus in north London following the win over Everton, but the Gunners are currently sixth, seven points behind fifth-placed Spurs and eight behind Chelsea.