They were trailing until the 87th minute, when a fortunate equaliser took the game into extra-time. They then had a usual suspect to thank for settling it, a brace from the Senegalese Andre Senghor taking them through. That double from Senghor spoilt the birthday gift Wahda had promised their influential and popular forward Ismail Matar, who turned 28 on Saturday.
In truth, though Baniyas left it late they were worthy winners and now have a chance to put some sheen on a disappointing season when they take on Al Jazira in the final on April 23 at Zayed Sports City, where they will face Al Jazira, who beat Sharjah 4-1 in the earlier last-four encounter. Baniyas have won the President's Cup just once before, twenty years ago in 1992.
Baniyas had shown initiative and drive throughout and effective as Matar was, Haboush Saleh, Baniyas' effervescent prompter, was an equal counterfoil. All of Baniyas' ingenuity came through Saleh, patrolling in an inside left position.
He linked up well with Ahmed Ali throughout the game and only a lack of precision in his finishing prevented Baniyas from scoring. He could have had two in the first half alone, his movement and wit buying him space inside the penalty area but both times he shot weakly at the goalkeeper.
He had set up Senghor in the 70th minute with a lovely through ball but Senghor, not at his sharpest then, could not put it away. Saleh was not to be denied.
He had scored the winning goal in the UAE Olympic team's win over Uzbekistan last month and it was a foul on him that led to the equaliser.
The Spaniard Francisco Yeste took the free kick, wide on the right and from the narrow angle, Moataz Abdullah should not have allowed it to slip in at his near post.
Matar did not deserve to lose and as belated birthday gifts go, winning a cup semi-final would not have been a bad one.
It was his deep, curving corner from the left seven minutes before the break that led to Wahda's goal. Mohammad Khalaf came out but failed to cleanly punch the ball away and the ball fell to the Brazilian midfielder Hugo who shot clean through a scramble of defenders.
And that was only Matar's most obvious contribution. The national team forward was ubiquitous in Wahda's best moments, floating around the opposition half, dropping deep, moving out wide on both flanks and slipping through the centre.
A wonderful turn after the hour, having brought a high ball down expertly, should have led to a second. But Mahmood Khamis, put through from Matar's pass, could only shoot over the crossbar with only the goalkeeper to beat.
They would come to rue that chance in extra time when a wonderful cross from the substitute Nawaf Mubarak on the right saw Senghor rise magnificently to head home.
Then, two minutes from the end he was put through by playmaker Yeste and this time he made no mistake, for his 14th goal of the season. Few have been as vital.
Hugo was sent off on the final whistle to compund Wahda's misery.
Follow us @SprtNationalUAE