Joel Sunday's 90th minute goal proved to be the difference between the two sides after Alfred Kemah (38th minute) had cancelled out Bengaluru and India midfielder Eugeneson Lyngdoh's 15th minute goal.
With Aizwal FC notching up a win, the onus now lies on Bengaluru FC to perform in the second leg of the fixture which is slated to for May 3.
Aizwal had earned the right to feature in the Federation Cup after finishing eighth in the nine-team I-League. Top eight teams of the I-League will play in home and away basis in the tournament.
"We had several chances, and could have led by four goals. There is a cent percent chance that we will have a comeback and get through this round," he said.
Aizawl FC's head coach Jahar Das was all smiles after the upset win.
"We deserved this win as we played a good game. We are looking forward to the second leg and will play to the best of our abilities," he said.
In the opening minutes of the match, it was Bengaluru FC who nearly took the lead with some fluent attacking football. Sunil Chhetri's threatening corner resulted in a coming together of bodies in the Aizwal FC penalty box, but the home side defence stood strong and made a goal line clearance to deny Bengaluru FC an early lead.
Aizawl had their first proper shot minutes later when Yuta had a try from 30 yards away, but the ball went over the bar.
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