From a comfortable 188 for 3, India slumped to 206 for 6 as Rahane and Hanuma Vihari (16) found the pace and swing generated by the pink ball under lights too hot to handle.
Ravichandran Ashwin (15 batting) and Wriddhiman saha (9 batting) saw off the final few overs and also got a few runs.
In conditions, which can't exactly be called batting friendly, India were doing well with a 88-run partnership between Kohli and Rahane (42 off 91 balls) during the final session. But fortunes tilted once Kohli was back in the pavilion.
Rahane was soon snapped with the second new ball by Mitchell Starc (2/49), easily the best bowler in action.