Sections of the Emirates Stadium appeared to boo the decision to bring on Andrey Arshavin in the midfielder's place.
"In last 15 to 20 minutes we had players who have given everything, players like Oxlade-Chamberlain and he was playing on the left and it didn't work out," Wenger told Sky Sports News
"You do not need to agree with it (the decision), you can understand that. I dont know how many thousands of substitutions I have made over the years, the fans do not always agree with them. I make decisions and I stand up for them."
The result has left the Gunners five points off the Champions League places.