ATKMB and Rajasthan United, who both have four points from three matches, will fight for the second quarterfinal spot from group B.
A two-goal blitz by substitute Lallianzuala Chhangte in the space of two minutes, following goals from Vikram Pratap Singh and Greg Stewart gave Mumbai City full points.
The win lifted Mumbai City FC to fifth spot, level on points with fourth-placed Jamshedpur FC. Mumbai City FC play Odisha FC on Sunday.