The pair had to be separated after Mancini reacted to Balotelli catching Scott Sinclair with a late challenge.
Although officials have attempted to play down the incident, which two sources have said was a "storm in a tea-cup", pictures indicate a clash of tempers, with Mancini appearing particularly animated and angry.
Members of the City coaching team dragged Balotelli away from his boss, who was shown to be pointing at the forward following the initial tackle.
Mancini is also seen grabbing Balotelli's orange bib as he made his feelings known, even though the younger man towers over the former Italy international.
City refused to comment yesterday, citing the public access around their training ground as the reason why what they regard as a relatively minor incident should cause such a stir.
Questions are bound to be asked of Mancini at his press conference to preview tomorrow's FA Cup tie with Watford though, with not just Balotelli's behaviour but his own coming under scrutiny.
Mancini has previously been criticised for indulging Balotelli far too often.
However, another example of him flying into a rage with a player hardly sets the greatest example either.
Having crashed out of the Champions League at the group stage for the second season running, and with City currently seven points adrift of United in the Premier League title race, there are question marks over Mancini's future anyway, with both Pep Guardiola and Jose Mourinho already mentioned as potential successors.
The former is already technically available, even if he is currently on a year-long sabbatical, while it is widely expected Mourinho will leave Real Madrid in the summer.
Sergio Aguero is set to miss tomorrow's game with the hamstring injury he suffered during Tuesday's 3-0 win over Stoke.
Pablo Zabaleta was among the scorers and while he appears to have cemented himself in the right-back role, the popular Argentina star insists he is taking nothing for granted.
"I'm just working hard to keep my place," said Zabaleta.