Aubameyang, 31, scored the Gunners' second goal in a 2-0 Premier League win at Newcastle on Sunday.
That was his first start since he contracted the illness while on international duty with Gabon and Aubameyang could now feature in Thursday's second leg clash with Spanish side Villarreal.
Aubameyang was on the field for 77 minutes at St James' Park last weekend. Asked about that significant stint in Tyneside, he told Arsenal's website: "At the end for the last five minutes, I was dying a little bit. But to tell the truth, I felt good the whole game, so I was really happy with that.
"I have to say that the doctors did incredible work with me, bringing me to the hospital and stuff like that. I'm really thankful for them."
Aubameyang added: "I have to say, when you are out for a few weeks you realise how good it is to be back on the pitch. I was really happy to be back first and scoring a goal."
Now Aubameyang, who returned to action as a late substitute in last week's 2-1 first leg defeat by Villarreal, is keen to take a significant role on Thursday in a match that could define Arsenal's season.
"It was really important to take some confidence and win this game. We know that we will need everyone to be ready on Thursday," he said.