Onana was changed at halftime for fellow former Evertonian Ross Barkley.
Emery later explained: "We have to be intelligent. Playing in matches, like the international players did before, getting today only one training session with us and playing again on Tuesday, we have to try and be clinical. We have to be intelligent, using each match the characteristics we need on the pitch.
"Ross Barkley and Youri Tielemans they are playing more or less similar. They can even play together with one other midfielder - Amadou Onana or Kamara - but when we needed in the second half to keep ball possession, taking time in the build up.
"I decided to change tactically for Onana. I told last week when you were asking me about him, he’s been really relevant with his impact in the squad but there’s still a lot of work to do, trying to get our ideas tactically and feel comfortable doing it.
"The players, they are joining us in the structure we are trying to build and it’s not easy for them to adapt quick. Amadou, he was doing quick because we didn’t have Kamara in the squad available to play. The characteristics of those players are more or less similar but they can play together.
"Today I decided the change tactically but of course, it was not for his mistake because I am never punishing the mistakes of the players. Never."