Despite expressing his exasperation with the controversial striker on numerous occasions, Mancini was ultimately fiercely loyal to the firebrand striker throughout his turbulent spell at City.
Mancini, who first gave Balotelli a chance at Inter Milan, brought the unpredictable forward to City in 2010 and stood by him after a series of misdemeanours on and off the field.
The manager even vowed to give Balotelli "another 100 chances" after a high-profile training-ground fight with him earlier this month but Milan's persistent interest in the player led to his departure.
After signing a four-and-a-half year contract at the San Siro, Balotelli revealed he said his farewells at City earlier this week.
He told the club's website: "I spoke with Roberto before I went to speak to the players.
"We spoke for some time about lots of things. He was sad, and I was too.
"But it was a good conversation. I love Roberto, he has been very important for my career, and I will always thank him for having trust and faith in me.
"Being at City was an important part of my life and career. I needed to grow up like a player and as a person and it has been a very good experience for me."
Balotelli scored 30 goals in 80 appearances for City and played key roles in the 2011 FA Cup success and last year's Premier League title win.
But despite that contribution the 22-year-old will be equally well remembered for four red cards, clashes with team-mates, brushes with discipline and other controversies.
The most recent of those, a challenge to a club fine which was later dropped and the bust-up with Mancini, sparked intense speculation he could leave.
That was consistently denied by City but Milan sensed an opportunity to lure the player to his boyhood club and a fee of £19million, rising to £22million, was agreed this week.
That leaves City just short of recouping the £24million they paid Inter for his services two-and-a-half years ago.
His departure was all but confirmed on Tuesday when Balotelli missed the champions' goalless draw with QPR at Loftus Road.
Balotelli said: "I will always be interested in Manchester City and their fortunes.
"I really hope that City can win the league again this year and beat United.
"I think there are great players at the club and a great manager too.
"The club will be very successful in the future and that makes me happy."
Balotelli became a cult figure at City as tales of an extraordinary private life, mostly thought apocryphal, complemented his performances.
He said: "For sure I will remember my brilliant team-mates, the manager and all the supporters.
"They are the best, they were great with me and I will always have a very special place in my heart for City, it's a great club with a great future.
"I thank them for all of their support of me. Maybe one day we will see each other again."
Balotelli's displays this season failed to build on those of previous years and, with other matters a distraction, Milan's offer evidently proved tempting.
He has scored just three goals this term, only one in the Premier League, and has made only two substitute appearances since a dismal display in the derby defeat by Manchester United on December 9.
It now remains to be seen whether he will go straight into the Milan squad for Sunday's Serie A game against Udinese at the San Siro.
He has already been pictured in Rossoneri colours and will be officially presented to the media as a Milan player on Friday.
News of his return to Italy sparked huge interest and he was swamped by reporters, photographers and fans as he arrived a clinic in Milan to undergo his medical on Wednesday.
There were also reports of police being called to disperse unruly crowds outside a restaurant where he met club officials.
He visited the club's training ground on Thursday morning and formally committed his future to Milan by signing a four-and-a-half year deal.
A statement read: "AC Milan announces that it has acquired from Manchester City Mario Balotelli, who has signed a contract until June 30, 2017."