Terry, and centre-half partner Branislav Ivanovic, looked vulnerable throughout the derby, but Villas-Boas denied the FA investigation had affected the performance of his team or their captain in any way.
"Has the situation affected John? No, not at all," Villas-Boas said.
"It hasn't distracted him at all, I don't think.
"For me, it was never a situation. It's a misunderstanding.
"It's an FA investigation, so let them investigate.
"This is just defeat for a team, a very important defeat and nothing else."