The 39-year-old will preside over the game along with assistants and compatriots Zakhele Siwela and Souru Phatsoane.
The anticipated one-off game will take place at Wydad's Mohammed V Stadium in Casablanca on 30 May.
Gomes, who has been recently picked as one of South Africa's representatives at the World Cup finals in Qatar, is one of the continent's most decorated officials.
He took charge of the African Nations Cup final last February, which Senegal won after beating record seven-time winners Egypt on penalties following a 0-0 draw.
Gomes took charge of another Ahly-Wydad duel in the return leg of the Champions League semi-final in 2020, which Ahly won 3-1.
Most recently, he refereed Wydad's 1-1 draw with Angola's Petro Atletico in the second leg of the Champions League semi-final earlier this month.
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