The Gabon striker has been left out of the squad for Arsenal's last two matches and revealed on social media on Thursday that he contracted the virus during the recent international break.
Aubameyang posted a picture of himself in a hospital bed and wearing a gown, but he has now been discharged and his health is improving.
Speaking at a news conference after Arsenal's 4-0 win over Slavia Prague on Thursday evening, which saw his side through to the Europa League semi-finals 5-1 on aggregate, Arteta said: "We just spoke with him. He's at home, he's fine.
"He had two days in hospital to get the right treatment, but he's feeling good now.