Blood tests have revealed the Arsenal captain contracted the disease while he was on international duty with Gabon last month.
Aubameyang did not travel with the Arsenal squad for their Europa League clash against Slavia Prague on Thursday night and is in hospital.
In an Instagram post, Aubameyang said: “Hey guys, thanks for all the messages and calls. Unfortunately I contracted Malaria whilst being on national team duty in Gabon a few weeks ago.
“I’ve spent a few days in hospital this week but I’m already feeling much better every day, thanks to the great doctors that detected and treated the virus so quickly.
“I wasn’t really feeling myself the last couple weeks but will be back stronger than ever soon!
“Will be watching my boys now, huge game for us! Let‘s go and get it Arsenal.”