Mourinho was due to manage an England XI including ex-Arsenal keeper David Seaman and former United defender Phil Neville, plus a host of celebrities.
The 53-year-old could still help train the squad and will be at Old Trafford for the game, although he might not be in the dug-out.
Sunderland manager Sam Allardyce takes over from Mourinho.
The match is Mourinho's first at Old Trafford since his appointment as Louis van Gaal's successor last month.
The former Chelsea, Inter Milan and Real Madrid boss visited United's Carrington training ground for the first time on Monday.
He was given a tour by executive vice-chairman Ed Woodward and met club legend Sir Bobby Charlton during his seven-hour visit.
Mourinho is yet to meet with Ryan Giggs. The Welshman still has a contract as an assistant manager, although Mourinho's long-time deputy Rui Faria is expected to be in that role next season.
Giggs, 42, is on leave until Saturday and is yet to be contacted by Mourinho or Woodward - and is still to be told what role, if any, they have for him.
Meanwhile, midfielder Michael Carrick is expected to stay on at United for another season. The 34-year-old is out of contract but a new one-year deal has been offered by the club.
Manchester United manager Jose Mourinho will no longer take charge of England for Sunday's Soccer Aid charity game.