Meulensteen was expected to depart Old Trafford following the arrival of David Moyes as Sir Alex Ferguson's successor and he follows backroom duo Mike Phelan and Eric Steele, who have also exited the club.
Moyes can now press on with plans to bring in his own coaching staff as he prepares for his first season as United manager.
Reports have suggested Meulensteen could link up with fellow Dutchman Guus Hiddink at Russian club Anzhi Makhachkala and he was also thought to be one of the contenders for the Wigan job.
Meulensteen spent five years at United as the coach of youth and reserve teams until 2006, but he soon returned for a second spell in 2007 and was quickly hired as first-team coach.
"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," he said.
"I wish everyone at this great football club all the best."
Executive vice-chairman Ed Woodward said: "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."