In the first match played at JRD Tata Sports Complex, Salgaocar and Mohun Bagan fought keenly to finish 1-1.
Topping the Group A with 10 points in the league stage, Salgaocar scored in 33rd minute through striker Albino Pereira, while Bagan striker Mayon Kaping restored parity when he converted a measured crosspiece from left flank in 85th minute.
Pune FC, who finished second with nine points in the league stage, came from behind and defeated Group C topper Sesa Goa, through first half goals in JRD Tata Sports Complex.
From another free kick from almost the same spot, Pune striker Subasish Bose equalised three minutes later.
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The defending champions struck the winner in 30th minute when forward Thongkhosiem Haokip headed home.
In the third match of the day, Somnath Nayek put East Bengal in the lead in 24th minute.
The red and gold brigade kept their defence in tact till TFA striker K Udanta Singh restored parity in the injury time.