His second opportunity saw the England worldwide head straight at Renan Ribeiro, but the striker landed badly on his ankle and left the field on a stretcher.
The Gunners are yet to confirm the exact nature of the issue, although it appears the forward is set to miss several months.
The 27-year-old striker was given oxygen on the field before being stretchered off with his right leg in a brace, as players from both sides watched on in distress.
The move to replace the manager was precipitated by Danny Welbeck's victor in Arsenal's 1-0 win over Sporting in Portugal two weeks ago at a raucous Estadio Jose Alvalade.
Rob Holding: "I didn't see it because obviously I'm at the other end of the pitch so I didn't see exactly what he'd done".
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Images showed Welbeck's right ankle bent at an unnatural angle, and Emery told his postmatch news conference: "The worst news tonight is this injury".
"Danny is a tough lad, so if he's on the floor, I know it's something serious".
"His injury was hard for the mentality of the players because they looked at the injury".
"This injury is very big for him, for us and for everyone". "We think [they are] serious injuries".
The incident knocked the wind out of Arsenal's sails but Welbeck's replacement Aubameyang hit the crossbar as the visitors offered very little in terms of an attacking threat.
"When one player suffers an injury like that the mind thinks of the player first".