Brazilian Diego Maurcio struck both goals for the winners in the first half.
Nandha Kumar bagged a brace as Odisha won 3-1 against NEUFC in the semifinal.
The result meant that Simon Grayson's men reached a third final of the 2022-23 season, having made the summit clash of both the Durand Cup and the Indian Super League.
In Group D, both NorthEast and Mumbai City FC finished with six points each, but the Guwahati side made the grade by virtue of their better head-to-head record.
FC Goa beat ATK Mohun Bagan 1-0 in the final Group C match.
Bengaluru advanced to the semifinals as group toppers with five points.
Chennaiyin and Churchill played out a goalles draw in the first match of the day.
Jamshedpur won 3-0 to finish top of Group C and enter the semifinals.
The visitors celebrated their winner by paying tribute to the late father of their captain Brandon Fernandes.
Hyderabad FC and East Bengal FC played out a thrilling 3-3 draw in the second match.