With the hosts losing skipper Gideon Waja, Majeed Ashimeru, Razak Abalora, Emma Boateng, Caleb Amankwah and Komlan Agbegniadan from the squad they started with last season, coach Klass Rasmunssen still had quality available after parading former Techiman City goalkeeper Richmond Ayi in post, alongside Alhassan Mohammed, Nuhu Musah, Francis Boateng and Aminu Mohammed.
Kotoko, on the other hand, missed the services of last season's poster boy Sadick Adams, but his place was taken by Yakubu Mohammed, with Keane Boahene playing behind him.
It was Wafa who had the first shot on goal in the first minute, after Richard Danso combined with Aminu and although, they had a free-kick just outside the box, the hosts couldn't make it count.
However, they made amends and shot in front two minutes later, as a powerful free-kick from Aminu went past goalkeeper Felix Annan, who was making a comeback to a venue where he was groomed.
Kotoko attempted to make a quick response with some decent string of passes but Wafa neutralised those efforts despite Frank Sarfo Gyamfi coming close several times.
However, by the 18th minute, it was all square and the away fans were in an ecstatic moment. Yakubu who was nearly offloaded during the transfer window following an abysmal performance on his debut season, turned from a villain to hero. The former goal king connected a shot from Jordan Opoku and it beat goalkeeper Richmond Ayi.
Four minutes later, Yakubu was played through by Boahene to put Kotoko in front for the first time in the game, but his last ditch effort went wide, while teammate Wahab Adams saw his header narrowly missing the target on 30th minute.
By the 49th minute, Wafa's Umar Bashir missed the brightest opportunity in the game. The youngster headed above the crossbar from a corner-kick, while Danso appealed for a penalty few minutes later following a challenge from a Kotoko defender but referee Charles Bulu ignored the appeals.
Kotoko brought on Mawuli Osei for Yakubu, in a bid to push for the match-winner but it was the hosts who turned the game on its head in the dying embers.
By the 88th minute, Kotoko nearly scored an own goal following a Emmanuel Owusu's missed kick but goalkeeper Annan sprawled to make a goal line save.
Kotoko will play Inter Allies next weekend at the Baba Yara Sports Stadium while Wafa travel to Accra to play Liberty Professionals.