The Portuguese is in awe of the Red Devils boss and the length of time for which he was in charge of the club but is not surprised by how well he did.
Mourinho told The Offisde Rule podcast: "We will all miss him and, for me, it will be difficult to go to Old Trafford, especially for the first time, to play against Manchester United without such a figure in the opposite dugout.
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"Everybody knows that the beginning was not easy for him. Everybody knows that it took him three or four years to win the first piece of silverware and United gave him the conditions to do an incredible job. After that he was unique, absolutely unique.
"The number of trophies he won for Manchester United in English football is absolutely amazing and to manage for more than 20 years is incredible."
Mourinho and Ferguson developed a great friendship during the former's time as Chelsea boss but the closeness started a year before that when he brought his Porto side over to play in the Champions League.
That game ended with the Portuguese side winning in injury time and the Madrid coach says that he was taken aback the Scot's graciousness in defeat.
"We scored in the last minute and we went through and it was not normal for me, not normal in the culture that I knew, that the opposition manager knocked on our dressing room door after the match - which was a moment when he would be very, very disappointed - and came in to congratulate me and invite me to go to his room for a glass of wine," Mourinho enthused.
"That marked our relationship. After that we played so many times with each other and the next year I moved to England with Chelsea. After that the relationship went in that direction - it didn't matter who won and who lost. The respect was always there."