Joseph (45+1 penalty and 52nd minute) continued his goalscoring spree to help a Kerala outfit win the oldest competition in Asia for the first time since FC Kochin won it 22 years ago.
City soccer giants Mohun Bagan, who last won the Durand Cup in 2000, have now lost in three finals on the trot (2004, 2009, 2019).
For the Mariners, Salva Chamorro (64th) scored a consolation goal.
It was tense in the final quarter as the hosts searched for a equaliser and even saw Gokulam go down to 10-men when Jestin George was shown a second yellow card for a foul on Lalchhawnkima in the 87th minute.
Mohun Bagan had a flurry of chances in both the halves but were guilty of spurning them as Gokulam Kerala held on after Joseph gave them the lead and added to his tally in the second half.
Mohun Bagan”s best chance to draw level came three minutes after Chamorro scored but Henry Kisekka failed to convert a brilliant cross.