The deal was pushed through in the final minutes of the transfer window and reunites United manager David Moyes with a player he knows well from his time at Goodison Park.
United have paid £27.5million to secure the services of the highly-rated Belgium international.
Moyes was unsure about whether United would be forced to pay the sum stated in the clause, which is why he allowed it to lapse.
As it turned out, with other targets disappearing over the course of the window, United's need became more desperate.
And with Everton chairman Bill Kenwright playing hardball after becoming annoyed at what he deemed to be a ridiculously low joint bid of £28million for Fellaini and Leighton Baines, which was described by Everton as "insulting and derisory", Moyes ended up paying £4million more.
It means Fellaini has become the fourth highest transfer in United's history, ahead of Wayne Rooney and behind only Dimitar Berbatov, Rio Ferdinand and Juan Sebastian Veron.
His 12 goals for Everton last term also underline the goal threat he can provide given, other than Shinji Kagawa, who scored six times, no midfielder managed more than two strikes for the Red Devils last term.
And despite the obvious frustration at missing out on so many targets, particularly Thiago Alcantara, Cesc Fabregas and Herrera, Moyes has at least been able to complete his first significant transfer since replacing Sir Alex Ferguson at the beginning of July.