Eisa Ahmed gave the home side a first-half lead and Papa Waigo doubled the advantage on the hour for a 2-0 victory at Al Nahyan stadium.
Ahmed powered home a header from a Srdan Andric free kick to set the platform for Wahda.
Waigo then tapped in the second unmarked at the far post after from the Croatian Andric's corner flew past several players to the Senegalese striker.
Any hopes of a comeback from Baniyas were dashed when Andre Senghor, their own Senegalese forward, was given a straight red card for a dangerous tackle on Adel Al Hosani, the Wahda goalkeeper, when he charged out of his position for a clearance.
"I am glad I was able to contribute to this win with a goal. I enjoyed that moment because I don't get to score that often," Ahmed, the Wahda defender, said in a post-match television interview.
"Everything went to plan tonight. We created more scoring opportunities, enjoyed more possession and controlled the game. I think we played one of our best matches so far and hope we can build on this performance.
"Baniyas came in to this game on the back of four wins and they were a pretty good side. It is still early days in the league with several teams in contention and I can say we are one of them."
Wahda turned it on after Ahmed had broken the deadlock with his second league goal. It triggered several attacking forays, yet Wahda failed to add to the score in the first half.
Marcelo Oliveira misjudged to connect a lobbed pass from Ismail Matar and Saeed Al Kathiri effort of another header off Waigo's cross went just wide of the far post.
Wahda had also come close earlier when Matar and Waigo, both failed to latch on to a low cross from Adel Basulaiman. Baniyas strengthened their attack with Mohamed Zidan, the Egypt international, seven minutes in to the second half.
His introduction did not bring any joy though, as Waigo doubled the lead soon after when he latched on to Andric's corner.
Baniyas came close to pulling one back before Senghor's sending off.
Al Hosani did well to push over a powerful shot from Amer Abdulrahman and Yousuf Jaber's effort ricocheted off the bar.
Wahda looked comfortably placed thereafter as they had the two-goal cushion and the numerical advantage.
The result took their tally to 12 points, equal with Baniyas at the top of the table, but behind on goal difference.
Wahda's next game is against Dibba Al Fujairah and they can be assured to be in the top four at least for another week.
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