Faria announced on Saturday evening that he will step down as his Portuguese compatriot's right-hand man this summer, bringing an end to their 17-year association.
Mourinho admits that he will be upset to see Faria move on after next weekend's FA Cup final against Chelsea, but has wished the ex-Chelsea, Porto, Inter Milan and Real Madrid assistant the best of luck.
"Seventeen years... in Leiria, Porto, London, Milan, Madrid, London again and Manchester. Training, playing, travelling, studying, laughing and also a few tears of happiness," he told the club's official website.
"Seventeen years and the kid is now a man. The intelligent student is now a football expert, ready for a successful career as a manager.
"I will miss my friend and that is the hardest thing for me, but his happiness is more important and, of course, I respect his decision, especially because I know that we will always be together. Be happy, brother!"
Faria started off his career as a fitness coach at Uniao Leiria before becoming Mourinho's assistant at Chelsea in 2004.