Jozef Chovanec's team, fourth in the Pro League, enjoyed the majority of possession in the early stages at the Baniyas Stadium and deservedly took the lead when Khalid Mubarak fired home on seven minutes.
However, Dhafra equalised five minutes later following Thamir Mohammed's challenge on Ali Al Hamadi inside the penalty area, the visiting striker dusting himself off to dispatch from the spot.
Mohammed promptly atoned for his mistake, though, restoring his side's advantage as Baniyas briefly seized control. Yet Dhafra again drew level when Al Hamadi notched his second on 71 minutes, although Fareed Ismail struck moments later to make it 3-2 Baniyas.
As Dhafra pushed for yet another equaliser Fawaz Awana, introduced late by Chovanec, guaranteed the win by netting Baniyas's fourth, two minutes from time.
Despite the defeat, Dhafra are on six points, three adrift of Baniyas and Wasl.
In the evening's other match, Dubai were held at home by Al Shaab as Group A's bottom two teams contested a 1-1 draw. The hosts thought they had secured three points when Ali Hassan netted just before the hour, but Nasser Khamis managed a 90th-minute strike.
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