The 25-year-old midfielder had been linked with a move to Old Trafford throughout the summer and was the subject of a failed £36million joint-bid with left-back Leighton Baines.
Having been given permission by Belgium to delay joining up with the national squad ahead of their World Cup qualifier with Scotland, Fellaini handed in a transfer request late on Monday in a bid to push through the move.
One hour after the transfer deadline passed at 11pm, it was revealed that United had eventually secured their man after completing the necessary paperwork.
Everton boss Roberto Martinez has been unhappy with United's pursuit of his players and called the original joint bid for Fellaini and Baines as "derisory and insulting", but it will be good news for United boss David Moyes who is reunited with his former player.
Fellaini leaves Goodison Park having joined them from Standard Liege six years ago for £15million.
It was a positive conclusion to what was a rather frustrating transfer window for Moyes whose only other signing in the summer was full-back Guillermo Varela, while he failed to sign Athletic Bilbao's Ander Herrera amid suggestions imposters posed as United officials.
United had also targeted a late loan swoop for Real Madrid's Fabio Coentrao but there was no confirmation of a deal in the hours after the deadline and it is understood they may not have completed the paperwork in time.
Moyes has nevertheless insisted that he has total faith in the squad already at his disposal as he plots United's Premier League title defence after succeeding Sir Alex Ferguson as manager.
"From what I saw of the players, I'm more than happy with the players I've got," he said after United's 1-0 loss to Liverpool on Sunday.
Everton, meanwhile, will be pleased that they managed to hold on to Baines and were also able to bring in three new players on deadline day.