Aubameyang missed the 1-0 FA Cup defeat at Southampton on Saturday as well as the 3-1 Premier League victory over Saints three days later.
Gunners boss Mikel Arteta dedicated Tuesday's win to the Gabon striker, with Arsenal's goalscorers all sending messages of support to Aubameyang with their celebrations.
"And of course, thanks to my Arsenal fam for the love yesterday! I'm more determined than ever to keep our momentum going!
"Thank you all again – I really am beyond blessed to receive this level of support and love from all of you and I can't wait to be back – PEA."
The PA news agency understands Arsenal will keep supporting Aubameyang and a decision has yet to be made whether he will return for Saturday's Premier League visit of Manchester United.