In reply to India's first innings of 250, Australia was dismissed for 235 in 98.4 overs. Only 10.4 overs were bowled in the first session and an early lunch was taken as rain returned at the Adelaide Oval.
Travis Head top-scored with 72 and equaled his highest test score. He received invaluable support from Nathan Lyon, who counterattacked with an unbeaten 24 from 28 balls.
India's four-pronged attack shared the wickets with paceman Jasprit Bumrah and spinner Ravichandran Ashwin picking up three wickets apiece.
After sweltering conditions during the opening two days, persistent drizzle delayed the third morning session by 45 minutes.
Australia resumed at 191 for 7 with Head on 61 not out and Mitchell Starc unbeaten on 8. Twenty minutes into the session, under the lights, Starc recklessly drove a full Bumrah delivery and edged to be caught behind.
Play was then interrupted for an hour due to rain.
Bumrah bowled with accuracy outside the off-stump to be India's main strike weapon. Head, the South Australia captain, looked assured and kept the runs ticking over by working the ball on the leg-side.
Lyon dominated the strike in his partnership with Head and frustrated India with several powerful cover drives to reduce the deficit.
Ashwin, who starred on day two, came on to bowl 30 minutes before lunch and was greeted by a cavalier sweep shot from Lyon to the boundary.
Lyon's counterattacking continued with a six off a hook shot from Mohammed Shami's first delivery. Two balls later, Head played away from his body to be caught behind and Josh Hazlewood fell first ball, leaving Shami on a hat track when Australia bats in its second innings.