The result lifted City to the top of the Premier League table for the first time since Sven-Goran Eriksson was in charge during the 2007-08 season - although Manchester United regained first place after they drew 1-1 with Birmingham in Tuesday's late kick-off.
"We are happy but I think we will only be top for three hours," added the City boss.
"It is important to be there at the end of the season, not now."
City won 3-1 at Newcastle on Boxing Day and Mancini made five changes to his team for the match against Villa as he rotates his squad through a busy period that see his team play four games in 11 days.
"It was important to defeat Villa after our win at Newcastle," he said. "[Making the changes] was a good decision because when you have two games in 48 hours it is very difficult."
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