Ferguson, 71, will retire at the end of season after 26 years in charge and will be replaced by David Moyes.
Mancini said: "It was a great honour to beat him at Old Trafford and I wish him good luck for his future.
"I don't think there'll be another manager like him. To win every trophy for 27 years is incredible situation."
"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," Mancini added.
"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."