The Germany international was on a list of names that Mourinho gave to executive vice-chairman Ed Woodward during the summer transfer window, but talks for Boateng never materialised until recently as the club were hopeful of landing one of their other targets.
With deadline day just around the corner, the decision makers at the club prepared an offer that could see former Manchester City star Boateng - who has been told that he is allowed to leave Bayern Munich this summer - move to Old Trafford ahead of the new season.
However, the latest reports from German publication Bild claim that Boateng has personally called Manchester United boss Mourinho to thank him for his interest and reject the move.
It is claimed that the 29-year-old came to his decision following talks with Bayern Munich's head coach, Niko Kovač. The Croatian wants to keep Boateng at the Allianz Arena next season, although a switch to Paris Saint-Germain this summer is still believed to be on the cards.
The reigning Ligue 1 champions have eyed up Boateng following the appointment of former Borussia Dortmund manager Thomas Tuchel.
It is now believed that Manchester United will turn their attention back to some other targets as the club scrambles to sign a new centre back before August 9. The likes of Harry Maguire, Yerry Mina and Toby Alderweireld have all been linked with a move to Old Trafford.