Fae, 40, was assistant when the tournament in the Ivory Coast kicked off last month but was handed the reigns after Frenchman Jean Louis Gasset was fired when the Ivorians lost two of their three group games.
They still managed to scrape into the knockout stages as the last of the four best third-placed finishers and went on to win the trophy as Fae engineered a remarkable comeback.
"Emerse Fae was until now interim coach. He is now confirmed as a permanent coach," said Ivorian Football Federation president Idriss Diallo at a function in Abidjan on Monday, the Ivorian media reported on Tuesday.
Fae's only previous coaching experience was with the juniors at French club Nice and as coach of the reserves at Clermont Foot.
The French-born former Ivorian international played for his country at three Cup of Nations and at the 2006 World Cup in Germany.
His first assignment will be friendly matches in March, which are still to be confirmed, and then 2026 World Cup qualifiers against Gabon and Kenya in June.