Just when Raja where about to celebrate a looming win, substitute Taher Mohamed Taher struck in the 90th minute to spark jubilant scenes at Al Rayyan Stadium.
Hamid Ahadad, who played against Ahly while at Cairo rivals Zamalek last season, gave Raja a 13th-minute lead as the Red Devils looked porous at the back and toothless upfront.
But Ahly were reinvigorated following the second-half introduction of wingers Taher and Ahmed Abdel-Kader as well as striker Mohamed Sherif.
In a nerve-wracking shootout, both sides converted their five spot kicks with some powerful shots that both keepers were unable to stop even when they guessed right.
However, Ahly settled the tie in their favor in the sudden death, with Akram Tawfik converting his penalty and Raja's Abdullah Madkour blasting his effort astonishingly high over.
Ahly, who won back-to-back African Champions League and Super Cup titles, are now five Super Cup triumphs clear of nearest challengers Zamalek.
Source: Al-Ahram Online