The decision was greeted by home boos after Mavididi have struck Leicester's equaliser.
“He’d run his race,” City boss Cooper said. “I can understand the fans’ frustration. I get that and accept it. He was excellent second half and we felt like our likely chances were going to come from that side.
“But he’d run his race physically, absolutely run his race. There’s nothing wrong with that, it’s normal for an attacking player to run out of steam. We just thought we would put fresh legs on and let Abdul (Fatawu) one or two moments. He got involved in winning a corner.
“We’re really happy with Stephy and he didn’t come off because of his performance, let’s be clear. He came off because he had to run a lot in the first half, not in the way we wanted him to, and that accumulated into the second half. He ran out of steam. That’s all it was.
“Sometimes you make decisions and after you think you may have not got it right. But the rationale was a clear one and probably something we’d do again. Stephy was excellent in the second half, it was just that he’d run his race physically.”