All five Australian bowlers claimed wickets with Mitchell Starc taking three for 43 while his new-ball partner Josh Hazlewood took two for 18 from eight overs
Fellow fast bowlers Sean Abbott and Michael Neser are also in the squad, with the series finely poised after Australia won the first Test in Adelaide and India the second in Melbourne.
It ended one of the 32-year-old's most important Test innings, having come to the crease with India in trouble at 64 for three to steer them into a strong position.
It was a determined and crucial knock against a world-class attack by the mild-mannered 32-year-old, who assumed the captaincy from Virat Kohli after he returned home for the birth of his first child.
But Cummins finally got the wicket he deserved when Gill, who added 17 to his overnight score after being preferred as opener to the axed Prithvi Shaw, got a nick and Paine took a simple catch.
Australia head into the Boxing Day clash at the Melbourne Cricket Ground on a high after crushing the visitors by eight wickets inside three days in the opening Test at Adelaide.