The Spanish head coach took off centre back Pau Torres, as they secured a 0-0 draw in the Netherlands.
Villa will now head to Villa Park next week to try and progress to the last eight of the Europa Conference League.
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"He had a small injury two weeks ago," Emery explained about Torres to reporters.
"We did a plan with him. I think tactically as well we needed to change something.
The plan was to play 45 minutes with Pau Torres."