Mancini said: "Maybe he is homesick but I don't think it's a long-term problem. He is 20, has left his family for the first time - it's normal to miss them.
"It is very important to keep him. He is a very good player and he can improve a lot."
City easily defeated an out-of-form Villa, with Balotelli scoring two superbly taken penalties as well as a close-range tap-in.
Great response to the critics from Mario Balotelli - a hat-trick and no histrionics
Beware the Moon Lads
The Italian played in the lone striker role as Argentine Carlos Tevez was rested - and underlined his qualities with a very good display.
"I think it is very important for the guys to help Mario. This season is a very important experience for him," added Mancini.
"If he plays like he did this afternoon he can be one of the top players in Europe."
City scored twice in the opening 13 minutes as they dominated a Villa side that has now won only two of their last 13 top-flight fixtures.
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.
However, Manchester United will regain first place if they avoid defeat against Birmingham when they meet on Tuesday (kick-off 2000 GMT).
"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 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."
Source: BBC Sport
Source: BBC Sport