The Spanish loanee was taken off during the second half, when the Gunners were struggling to retain control over the game.
Some fans criticised the decision, believing the sub only made the team worse.
But Emery defended his choices, saying to the club's official website: "But today it was very, very hot. We needed in the second half, some fresh players.
"We were struggling second half and I was thinking how we can improve with three players, fresh players, for give us more energy and give us also more capacity to be strong physically and tactically and also technically."