Arhima defenders gave NISA a tough fight in the first half till in the 44th minute when Mani Mohan Singh scored to give the lead for the Imphal club.
Down 0-1, the Meghalaya side tried their best to bring the match on an even keel and their efforts bore fruit when Stevenfield Lenong scored the equaliser in the 77th minute.
The 1-1 stalemate prevailed in the full time and it was in the eighth minute of the extra time that NISA converted a penalty to settle the issue.
Thomas Singh converted the penalty after an Arhima defender handled the ball.