Mourinho dropped the popular Casillas in the 2012-13 campaign, dividing the fan base in his turbulent third season at the Santiago Bernabeu, which ultimately precipitated an exit for the club captain in 2015.
But, after news of the 39-year-old's retirement, Mourinho told AS: "His intelligence and maturity meant that we have always respected each other and years later, we have even been able to cultivate an honest friendship."
Casillas was first choice for the Portuguese in 20010-11 and 2011-12, when Los Blancos won the Copa del Rey and then LaLiga with a record 100 points.
"Iker is one of the greatest goalkeepers in Real Madrid's history, in Spain's history and world football history," Mourinho added.
"With him, we won the league which broke all records and we also had some difficult moments because of a decision which I took – a professional decision, not a personal one, to play someone else in goal."
The Madrid legend was initially dropped for Antonio Adan and, after suffering an injury, was later replaced by January signing Diego Lopez.
Last year, Mourinho revealed he had been in touch with his former club Porto following the news that Casillas had suffered a heart attack and the goalkeeper then praised the Portuguese on Twitter for his tactics as Spurs came back to beat Olympiacos in November.