The 25-year-old Belgian international had been linked with the Red Devils all summer and was part of a failed combined bid of $56 million (£36m) with England left-back Leighton Baines.
Fellaini was given permission by his national team to link up with the squad later than everyone else so he was able to hand in his transfer request to Everton and push a move through to Manchester United.
Fellaini leaves Goodison Park after 6 years were he was initially bought for $23 million (£15m) from Standard Liege.
United failed to prise away Fabregas from Barcelona and failed in their attempt to lure Thiago Alcantara to them as he later chose to link up with his former manager Pep Guardiola at Bayern Munich.
Reports were also circulating in the final hours of the transfer window that United were interested in taking Real Madrid full-back Fabio Coentrao on a season long loan, but nothing ever materialized from that.
Manager David Moyes has previously insisted that he is happy with the squad at his disposal saying after the 1-0 defeat to Liverpool:
From what I saw of the players, I'm more than happy with the players I've got.
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