Samad Ali Mallick had given East Bengal the lead in the 18th minute with a superb 40-yard strike.
The red and golds looked good to hold on to the slender lead before Mehtab Singh brought down Mohamed Irshad inside the box in the second half stoppage time to award Gokulam a penalty which was converted by Marcus Joseph to take the game to extra time.
Mehtab was given marching orders for his act and East Bengal were down to ten men.
As both the outfits could still not be separated, it took a tie-breaker to decide who plays the final on Saturday.
For East Bengal, skipper Lalrindika Ralte hit the post with his first attempt while Jaime Colado and Naorem Tondomba Singh also saw their attempts saved by former East Bengal custodian Ubaid CK in the Gokulam goal.
For Gokulam, Bruno Pelissari, Justin George and Lalromawia were on target from the spot.
The match was off to a feisty start but East Bengal slowly started to dominate the midfield with Pintu Mahata and Mallick combining well.
The home team were rewarded for their repeated forays in the 18th minute when Mallick's long-ranger took a slight deflection off Mohammad Rashid and nestled into the back of the net.
East Bengal led 1-0 at halftime and looked good to hold on to the advantage as Gokulam showed little intent with Joseph lacking support.
But in the dying minutes of the second half, the away side got a penalty and Joseph made no mistake from 12 yards.
In extra time, East Bengal were defensive as they were a man down while Gokulam tried to take advantage and surge ahead for the first time in the game. But in the end, it was down to luck as the penalties came calling.
( With inputs from IANS )