SunSport exclusively revealed that the Portuguese has been lined up as a potential replacement for departing Arsenal boss Arsene Wenger.
Just this month the Special One backed his assistant to succeed as Arsenal boss and would not stand in his way.
Manchester United revealed the news on their website with a statement from Faria that read: "After a lot of consideration, and with a very heavy heart, I have decided the time is right for me to move on.
“I have had 17 years of incredible and unforgettable experiences.
"However, I have felt for some time that I would like to spend much more quality time with my family before pursuing any new challenge in my professional life.
“My heartfelt thanks go to the manager, Jose Mourinho, for the belief he had in me, all those years ago, when it all was just a student dream. I would like to thank him for the opportunity and confidence, for the knowledge and experience, but most importantly for his friendship.
“I would also like to thank Manchester United and all the clubs where I have had the privilege of working during this period. I would like to say a big ‘thank you’ to all the staff and players who, in different ways, have made an important contribution to my growth as a person and as a professional.
BON VOYAGE Arsene Wenger stone-faced as he takes charge of Arsenal training for the final time ahead of Huddersfield clash
“I wish you all the best for the future, knowing that you will always be my close friends.”
Mourinho added that he is now ready for a "successful career in management."
The United gaffer said: "17 years… in Leiria, Porto, London, Milan, Madrid, London again and Manchester. Training, playing, travelling, studying, laughing and also a few tears of happiness.
“17 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!”
Arsenal are understood to have designed a template for an “elegant” manager to replace Wenger and who can place the club’s interests ahead of their own.
Juventus boss Max Allegri remains favourite and have held talks with the Italian.
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