Mancini's arrival at the Etihad Stadium in December 2009 has coincided with a resurgence in the rivalry between City and Ferguson's Manchester United at the top of the Barclays Premier League.
"For me, it has been a great honour and pleasure to compete against Sir Alex for three years," Mancini said.
"It was a great honour to beat him in Old Trafford and I wish him good luck for his future. I don't know for which reasons (he has retired).
"Everyone can have his opinion but one manager who stays for 27 years in the same club and won every trophy for 27 years - it is an incredible situation.
"I don't think there will be another manager like him. It is difficult to say Sir Alex is the best (ever) but he is the best in the last 27 years."
Ferguson's retirement will leave a big hole for his replacement David Moyes, the current Everton boss, to fill but Mancini knows he cannot expect the balance of power to shift back in City's favour.
The Italian said: "I don't think this. At a top club, a big club like United, you can change the manager. Sir Alex built this team but it is a big club with a big history and I don't think it will change something."
Mancini, who added that he had sent Ferguson a message since he announced his decision, will now need to get the better of Moyes, a task he has struggled with when up against Everton. Moyes' Everton sides have beaten City six times in their last eight meetings while the pair were also involved in a touchline scuffle three years ago.
Mancini, who is preparing his side for this weekend's FA Cup final against Wigan, said: "It is better we can talk about this if we can play the Community Shield against United next year."
- Sports & Recreation
- Manchester United