Palhinha, 28, was given permission to fly to Germany on the understanding a replacement would have to be signed before the transfer would be approved.
But Fulham were unable to bring anyone in and the German transfer window shut at 17:00 BST with no deal signed off.
The collapse of the Palhinha deal will be a bitter disappointment to the Portugal midfielder, who had set his sights on playing Champions League football, and also to Bayern coach Thomas Tuchel, who saw him as a key acquisition after signing England captain Harry Kane.
Bayern were prepared to offer what would have been a club-record figure for a Fulham sale, with a fee in excess of £65m touted, but the Cottagers stood firm and refused to part with one of their most influential players until they had strengthened that area of Marco Silva's team.
Iwobi has played in two of Everton's three Premier League games this season, but missed Saturday's home defeat by Wolves with injury. The Toffees are yet to pick up a single point so far.
The 27-year-old Nigeria midfielder joined Everton from Arsenal in the summer of 2019 and has made 123 league appearances, scoring six times.
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