The match was the striker's first since leading Ghana to the semi-finals of the recent Africa Cup of Nations in Gabon.
The 31-year-old netted in the 83rd minute, moments after coming on as an 81st minute substitute in the game played at the Sheikh Hamdan Bin Rashid Al Maktoum Stadium.
Ahmed Khalil opened the scoring in the 28th minute, before finding target again on 76 minutes following an assist by Everton Ribeiro.
Wednesday's goal takes Gyan's season tally to three in nine league matches, with Ahli sitting second on the log.
The former Sunderland man is on a season-long loan from Chinese outfit Shanghai SIPG.