The Germany international was left out of the 4-1 win over Sunderland following a below-par performance against Bayern Munich in the Champions League that saw the 25-year-old miss from the penalty spot.
Wenger responded to suggestions that Ozil had been dropped due to poor form by insisting the midfielder was recovering from a dead leg and has now confirmed that he will, along with Thomas Vermaelen, return for the meeting with Stoke.
The Gunners boss told reporters: "Vermaelen and Ozil are back in the squad, we have doubts over [Nacho] Monreal and [Kieran] Gibbs.
"Ozil had a difficult game [against Bayern] and sometimes it's good to refresh when you are under pressure."
Wenger also commented on Joel Campbell following the Olympiakos striker's impressive performance that saw him score his side's second goal in the 2-0 win over Manchester United on Tuesday.
He said: "Campbell was convincing going forward and he looks like he has adapted physically."