The Iranian team will face the winner of Port FC-AGMK FC quarter-final on Thursday to keep its hopes of back-to-back titles alive.
Mes Sungun got off to a rousing start when it scored in the third minute thanks to Mehdi Javid’s long-range effort off captain Fakhim’s corner.
The Lebanese side, however, drew level when Dragan Tomic beat Mohammad Shajari on the left before feeding Ali Tneich to score from above the arc.
Bank of Beirut had been shading possession and took the lead when Tomic set up Ali El Homsi to score from above the arc.
A desperate Mes Sungun deployed the power play with four minutes left in the game and was rewarded in the 38th minute through Javid’s strike from inside the box to force extra-time.
Fakhim then shook off his marker and scored from above the arc to give Mes Sungun the lead.
Bank of Beirut pushed hard in the remaining minutes but the equalizer was not to be as Mes Sungun advanced to the semi-finals.