He will miss the semi-final clash against Nigeria at the Cairo International Stadium on Sunday.
Atal was injured in the 30th minute of the quarter-final game against Ivory Coast and further medical examinations have confirmed it to be fractured collarbone.
He was replaced by Mehdi Zeffane as the Desert Foxes advanced to the semis via a penalty shoot-out.
Atal has been one of the key players in Djamel Belmadi's side and a constant menace down the right flank with his strong runs, which posed a threat to opposition's defence.
The Nice defender played four games in Egypt and has an assist to his credit.
"It's not easy to stop this Afcon at this level but I have full confidence in this group, we will still fight until the last moment," Atal tweeted.
Salam , merci pour tt vos messages . Hamdoullah c’est le mektoub , c’est pas facile d’arrêter cette CAN à ce niveau là mais j’ai totalement confiance a ce groupe on va encore se battre jusqu’au dernier moment . Inchallah on va rendre tt le peuple algérien fier ♥️🇩🇿 pic.twitter.com/sbkK8zsaRP— Youcef Attal (@YoucefAttal) July 12, 2019
Sunday's encounter will be the ninth time Algeria will play against the Super Eagles in the continental competition. The record is evenly balanced with three wins each and two draws.