The Australian makes only his second appearance for the Gunners since joining on loan from Brighton in January.
Bernd Leno is on the bench.
Granit Xhaka continues at left-back, while Gabriel Martinelli makes back-to-back Premier League starts and Hector Bellerin comes in at right-back.
Emile Smith Rowe has been handed another start after his brilliant display against Slavia Prague.
Aubameyang contracted the disease while on international duty with Gabon last month and he was in hospital for two days this week.
The forward is now back at home but is not yet fit to return.
In his absence, Alexandre Lacazette leads the line and captains the team once again.
Arsenal confirmed line-up: Ryan, Bellerin, Holding, Gabriel, Xhaka, Elneny, Ceballos, Saka, Smith Rowe, Martinelli, Lacazette.
Subs: Leno, Cedic, Chambers, Mari, Partey, Willian, Pepe, Nelson, Nketiah.
Date: Sunday1.30pm GMT, Sky Sports
Venue: Emirates Stadium
Referee: Craig Pawson