After the game ended 0-0 in normal time, Minerva Punjab won 4-2 in the shootout at the Nagoa Sports Complex in Goa on Tuesday.
Minerva Punjab had the better of the chances in the first half but a failure to convert them meant the teams entered the break level. However, Aizawl defended stoutly to stretch the tie into the tie-breaker.
Ajitkumar Meetei, Abishek Verma, Bijo Singh and Thoiba Singh scored for Minerva while Lalchhanhima Sailo missed in the penalty shootout.
As for Aizawl, only David Ramtharlawma and R Lalruatkima scored with Lal Famikima and C Laiphei failing to hit the target.
Minerva Punjab, who won both the previous editions of the tournament, will take on DSK Shivajians in the summit clash on Thursday.