Aizawl, who finished eighth out of nine teams in the just-concluded I-League, led 2-1 at half time through a double strike from Joel Sunday in the 26th and 37th minutes while C K Vineeth scored for Bengaluru in the 28th minute.
David Lalrinmuana (73rd) scored the third goal for Aizawl while star India striker Sunil Chhetri reduced the deficit to 2-3 for Bengaluru in the 74th minute.
In the end, Aizawl stormed into the semifinals on 5-3 aggregate in the home and away tie and knock Bengaluru out of the tournament.
Aizawl took the lead through Sunday, who shot the ball past goalkeeper Amrinder Singh in the 26th minute.
More From This Section
Within two minutes of Aizawl bulging the net, Bengaluru struck back as Vineeth took advantage of a poor clearance and shot the ball home.
Aizawl came back strongly to take lead for the second time in the match, after Sunday netted his second goal off a clever pass from Jaryan in the 37th minute.
After several attacks, Chhetri reduced the deficit (2-3) after he sent Aizawl goalkeeper Poirei the wrong way off a penalty kick in the 74th minute.
Thereafter, Bengaluru tried to create something but were denied by some resolute defending by Poirei in dying minutes.
Chhteri nearly missed an equaliser in the 88th minute when he was inches away from poking the ball home off a Kim Song Yong pass.