The Belgian heads to Old Trafford for a £27.5 million fee, where he is reunited with former manager David Moyes.
Goal understands that the deal was verbally agreed on Monday morning but United were made to wait on movements from the Toffees to bring in replacements.
Fellaini submitted a transfer request in the evening to waive any loyalty-bonus payment in order to ease the move and now, with Wigan's James McCarthy and Manchester City's Gareth Barry also confirmed at Goodison Park, the transfer has been pushed through.
United had also hoped to sign Leighton Baines from Moyes's former club but the Toffees rebuffed their advances throughout the summer, with the Premier League champions never meeting their £20m valuation of the left-back.
The Red Devils' other midfield target on deadline day, Athletic Bilbao's Ander Herrera, did not make the move, however, as United failed to meet the Basque's release clause.
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