It was widely anticipated the Dutchman would decline David Moyes' offer of a backroom job with the Red Devils and he has now become the third senior member of Sir Alex Ferguson's coaching staff to leave since the Scot's own departure last month.
"I would like to thank Sir Alex Ferguson, the owners, all colleagues, players and fans who made my time at Manchester United very special and one I will never forget," said Meulensteen.
"I wish everyone at this great football club all the best."
Executive vice-chairman Ed Woodward added: "I'd like to thank Rene for his contribution to the club, particularly since he returned to Old Trafford in 2007.
"He has been first-team coach for five years and in that time he has given great assistance to Alex and Mike Phelan in keeping the team at the top of the game, not only in this country but in Europe as well. On behalf of everyone at United, I wish him well for the future."
It means Moyes will be forced to look elsewhere for help to guide him through any unexpected problems during his early days at United, which may involve Wayne Rooney, whom he will meet after the striker spends the weekend at Glastonbury.
Paris Saint-Germain, Barcelona, Bayern Munich, Chelsea and Arsenal have all been linked with the England forward at times this summer, whilst it has also been stated Moyes would prefer to keep the player he introduced to senior football whilst at Everton.
If that is Moyes' wish, it is unlikely to be fulfilled without some sort of clarification on the supposed transfer request Ferguson claimed Rooney had made at the end of last season.
It has now been established Rooney did not express any such desire, merely sought clarification about his status with Ferguson.