City returned to winning ways thanks to Pablo Zabaleta's first goal for the club in the 51st minute.
However, a minute later Richard Dunne was sent off by referee Lee Mason after lashing out at Amr Zaki and City just managed to hold out for a vital victory.
Hughes said: "Richard has held his hands up. He has reacted to a challenge.
"It was the second time Zaki had caught him across the face. He has retaliated, the referee has seen it and we accept it."
The potential £107million deal for Kaka has dominated the headlines this week and Hughes added: "It has been a difficult week preparing the team considering the interest (about Kaka) around the club.
"But we really stuck at our task. We had to dig in and beat a side that has been in arguably as good form as any recently in the Premier League."