Manchester City's football administrator Brian Marwood was forced to intervene after boss Mancini threatened to fire physio Jamie Murphy.
Mancini is furious with City's medical department over the club's crippling injury list. He laid into Murphy, a popular figure with City's players, just hours before their Carling Cup defeat against West Brom.
The row on Tuesday was so heated that at one stage Murphy believed that he would not be travelling to the Hawthorns.
But Marwood has acted as peacemaker in the incredible dispute and Murphy continues to work at the club.
Despite yesterday's excellent result, City still have a number of star players on the injured list.
Left-back Alexsandr Kolarov, signed from Lazio in the summer, has been caught in the crossfire.
Kolarov has been wearing a protective ankle boot after surgery, but the club received a letter this week from his specialist.
The surgeon is no longer willing to take responsibility for Kolarov's rehabilitation after City put pressure on him to return.
Only last week £170,000- a-week striker Emmanuel Adebayor was involved in a row at the training ground with Mancini over the timescale for his return.
Adebayor showed a scan of his torn thigh muscle to the City manager as proof that he couldn't play.
The City striker finally returned to action yesterday as a late substitute for Carlos Tevez. City have a lengthy injury list, with Wayne Bridge, Mario Balotelli and Micah Richards all crocked.
Joleon Lescott was instructed to train last week despite a long-standing problem with his knees.
Lescott was on the bench yesterday and Jerome Boateng recovered from a knee injury to appear as substitute.
A City insider said: "The lads love Murphy and believe he has one of the best medical departments in the Premier League.
"Mancini and him just don't see eye to eye and it all blew up. The manager told Murphy 'we're done' - he thought he'd been sacked.
"As usual Marwood had to sort it all out."