The Turkish captain missed his side's stunning comeback victory over co-hosts Switzerland in Basle with a hamstring injury, but still looks to have played his last game in Euro 2008.
It had been reported that Zico's sacking threatened the £4million Emre deal that had been set up by the Brazilian coach.
The Fenerbache president Aziz Yildrim insists a deal has been struck and there is no going back.