Ozil, making just his third start of the season, was a huge influence in the away side’s creativity as they went 3-1 and 4-2 ahead, before his ‘planned’ substitution in the 65th minute with the score at 4-4.
"We can be proud of our work but not the result. Mesut Ozil is back helping us with his quality and his spirit. He played with good spirit, quality.
"It was in the plan to replace him, we had spoken about that before."
Arsenal eventually lost 5-4 on penalties after Divock Origi scored a 94th minute equaliser to make it 5-5 and take the game to a penalty shootout.
Emery thought his side deserved more from the game but added there were good points to take away from the defeat.
"A crazy match. I am very proud of their work, we had a high rhythm in the first 45 minutes. At the end we were winning until the last action. Penalties are 50/50 and we lost.
"We are sad but our work, we deserve to have more. There are lots of positives to take.
"Defensively, both teams cannot be happy with that. But for the supporters it was an amazing 90 minutes. The result was always changing. It was spectacular."
Club captain Granit Xhaka appeared to swear at Arsenal supporters after he was substituted during their Premier League draw against Crystal Palace at the weekend.
Emery has since suggested that the player should apologise after his reaction and was coy on the subject of him being involved in their match with Wolves on Saturday.
"Granit Xhaka? Now I cannot say how we are going to play on Saturday. We have to take it step by step."
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