Mancini described Ferguson as one of a kind after the 71-year-old announced he would retire at the end of this season following almost 27 years in charge at Old Trafford.
"It is his decision," said Mancini, who also revealed he sent Ferguson a message following the news.
"For me, it has been a great honour and pleasure to compete against Sir Alex for three years. 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 is retiring).
"He's a top manager but he took this decision and we should respect it.
"This is difficult (to say who is the best manager). Everyone can have his opinion but one manager who stays for 27 years in the same club and won every trophy for 27 years is an incredible situation.
"I don't think there will be another manager like him, In Europe, there are other good managers. I don't know if you can say Sir Alex is the best (ever) but he is the best in the last 27 years."
David Moyes will replace Ferguson and Mancini dismissed concerns that the change could hinder United's ability to challenge for major trophies.
"I don't think this. 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."