The deal for Fellaini went through in the final minutes before the deadline and reunites United manager David Moyes with a player he knows well from his time at Goodison Park.
United have paid £27.5 million 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 £28m for Fellaini and Leighton Baines, which was described by Everton as "insulting and derisory", Moyes ended up paying £4m more.
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.
Earlier, United's attempts to sign Athletic Bilbao midfielder Herrera descended into farce.
Moyes identified Herrera as a potential target and it was believed United were willing to pay Athletic's 36 million euro (£30.5 million) asking price.
It then appeared three United officials had arrived at La Liga headquarters in Madrid to complete the formalities that would allow Herrera to finalise a move to Old Trafford.
However, it now seems the trio were imposters and had nothing to do with United at all.
Subsequently, United withdrew from the transfer, even though it was established they had an additional hour to conclude the deal providing a Deal Sheet with the signature of both clubs and the player was submitted to the Premier League.
Insiders claimed that Moyes felt the buyout clause was too high and attempts to try and bring the fee down failed.