Yakubu was expected back at Goodison on Wednesday following Nigeria's quarter-final elimination by tournament hosts Ghana but did not turn up until Friday, Everton said on their official Web site (www.evertonfc.com).
Manager David Moyes declined, however, to reveal whether Yakubu, Everton's leading scorer with nine Premier league goals, would be punished in any other way for his unauthorised late return.
"All I would say is that it is an internal matter," Moyes told the Web site.
"Yak has been in this morning, I have spoken to him and he won't be included in tomorrow's squad."
Yakubu's Nigeria team mate Joseph Yobo was back at Everton by Wednesday's deadline.
Everton made no mention of whether Yakubu would return to the squad for Tuesday's UEFA Cup round of 32, first leg away to Brann Bergen of Norway.
Yakubu scored two of Nigeria's paltry tally of three goals in their disappointing Nations Cup tournament.
(Reporting by Rex Gowar, editing by Justin Palmer)
