Balotelli, 20, reacted angrily to a tackle from behind by the 22-year-old Germany defender, who retaliated by grabbing the striker by the throat in front of manager Roberto Mancini and the rest of the squad.
Enlarge Wild: Mario Balotelli (left) tussles with Jerome Boateng at City's training ground
The two players appeared to make up afterwards but Mancini had words with his £23million signing from Inter Milan as he tried to calm him down.
The confrontation will raise more concerns over Balotelli's suspect temperament after he was sent off for lashing out at West Brom last month.
A City official insisted: 'It was a minor flare-up lasting a few seconds and a reflection of the competitive edge the players apply to training every day. It's not something we are remotely concerned about.'
However, questions will once again be asked about the harmony in Mancini's dressing room following spats involving Emmanuel Adebayor and Vincent Kompany, and James Milner and Yaya Toure this season.
Enlarge Enlarge Bust-up: Boateng catches his breath after the scrap (left) before making up with Balotelli
The City boss also has to contend with the discontent among highly paid stars unhappy at being left out of the team. Joleon Lescott became the latest to speak out.
Lescott was a regular under former boss Mark Hughes, but he has made just five Premier League starts this season and is expected to drop to the bench against Bolton today after playing in the Europa League win over Salzburg.
'Of course. I'm not happy with the situation,' said Lescott. 'I don't enjoy sitting on the bench, and sometimes not even making the bench.'
Enlarge Dressing down: Roberto Mancini speaks to Balotelli after his clash ay Carrington
The England defender admits he is concerned about his international prospects if he is not a City regular, and might be open to a loan move next month.
'That's down to me and the club,' he added. 'The club might say, "If there's a chance to play, go and play". If not, I will have to stay here.
'Fabio Capello has kept his confidence in me and I'm grateful for that. But there's going to come a time when, if I'm not playing for City, I'm not going to be in the England squad.'
Manchester City and Chelsea target Luiz hints at leaving Benfica in JanuaryLescott fears he may have to leave Man City to save his England careerMANCHESTER CITY FC