Relebohile Mofokeng had given the Buccaneers the lead eight minutes after halftime before Hussein El Shahat equalised for the Egyptian giants but Mabasa made sure the South African side took maximum points from the contest.
The victory sees Pirates end the group stage unbeaten with four wins and two draws to take 14 points from six matches while Al Ahly also qualify for the next round with 10 points.
The Soweto giants started the game on the front foot and had an opportunity to open scoring as early as the second minute but Mofokeng opted for a square pass when the shot was on.
Dean Hotto also went close but saw his toe-poke balloon over the cross-bar.
The hosts then had their own chance to make Pirates for the earlier misses when Yasser Ahmed saw a header go wide while visiting goalkeeper Sipho Chaine then pulled off a great save to deny Khaled Abdel Fattah.
The South African outfit took the lea after the haftime interval when Mofokeng took advantage of a mixup at the back by the Al-Ahly defenders and calmly slotted the ball past Mostafa Shoubir.
The lead only lasted 10 minutes though when Aly Elshahat beat the offside trap and chipped over Chaine to make it 1-1.
Just as it seemed the game would end in a stalemate, Mabasa came off the bench and netted with a brilliant header with seven minutes of regulation time remaining.
