In the interim, former al-Ahly coach Mohamed Youssef would take charge of the national side, which was knocked out of the competition last week in a dramatic penalty shoot-out against the Democratic Republic of Congo.
The loss in the last 16 was a bitter pill for the Egyptians, who had gone to Ivory Coast hoping to win a first Cup of Nations since 2010, a year before talisman Mohamed Salah made his senior international debut.
The team had already lost the Liverpool star to a hamstring injury, after what local pundits called a lacklustre group stage performance with three draws.
The EFA had last week “apologised” to Egyptian fans for “not achieving their ambitions”.
Vitoria, whose tenure with the Pharoahs lasted under two years, is among a host of AFCON coaches on their way out.
The tournament has been a success for the continent’s underdogs, and disappointing for its heavyweights.
The five top-ranked African nations were all knocked out before the quarter-finals, as well as the four semi-finalists from the last edition.