At the break, Usman Khawaja was unbeaten on 21 runs (off 86 balls), while Shaun Marsh was batting on 1. Australia still trail by 193 runs.
Mohammed Shami (6) showed no patience at all, and went after a short delivery from Josh Hazlewood (3/52) only to be caught behind down leg side, as India's first innings came to a quick end.
Mitchell Starc (2/63), Pat Cummins (2/49) and Nathan Lyon (2/83) finished with two wickets each.
Thereafter, Australia did not have the best of starts as Ishant Sharma (1/9) bowled Aaron Finch (0) with a fuller, inswinging delivery on only the third ball of their innings.
The duo batted out 20.4 overs and put on 45 runs for the second wicket, already higher than any partnership for the top-four Indian wickets.
Indian pacers bowled with fiery pace, with Jasprit Bumrah (0/24) even breaching the 150km/hr mark at one point. However, they bowled short of good length on most occasions and did not make the Australian batsmen play too many deliveries.
Ravichandran Ashwin (1/15) was introduced into the attack in the 12th over of the innings, and immediately hit up an interesting duel with Harris. The cover drive came out against the spinner, expectedly as a few more runs started flowing.
Shami though bowled only four overs in the session, and even called on the physio at one point, to look at his bowling hand for cramps. He was off the field for three overs thereafter but word from team management is that he is fully fit. Even so, he did not bowl again in the session.
Ashwin then struck before lunch. Harris played on to his pads and was caught at silly point in the 22nd over, as the spinner got dividends for blocking all scoring opportunities.
Australia's 50 came up in the 27th over thereafter.
On day one, Cheteshwar Pujara's (123) 16th Test hundred saved India the blushes, after they were reduced to 86-5 at one stage.
(With inputs from agencies.)