However, the wicket came only after the two had added 50 runs for the seventh wicket.
But Lyon delivered another blow shortly before tea when Rishabh Pant edged one to the slip cordon.
As if that was not enough, Kohli could not stop himself from driving at a ball that was angling away from him.
Cummins faced 44 balls until then but it didn't matter as Bumrah trapped him LBW.
It's been 24 years since an Australian team batted as slowly in the first innings as Tim Paine's did on day two in Adelaide. On a day when Australia's four pacers operated as a unit, Pujara's calm application on an Adelaide wicket offering extra bounce was a sight to behold. In the very first over, he went for a wild slash but ended up playing on as Australia were reduced to 59/3.
He also stitched a 21-run and 40-run partnership with tail-enders Ishant Sharma and Mohammed Shami which helped India reach the 250-run mark. "We got the wickets the way we thought we might get the wickets", Saker told the Seven Network. The left-hander had been tied down and was content eating up deliveries. Ashwin led the attack from the front, bowling unchanged through the session from one end.
Head then joined Handscomb and defied the Indian bowling, which didn't allow any easy runs but also couldn't find another breakthrough before the tea break. They trail by 59 runs.
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"You can only put the bowlers under pressure if they give you the opportunity to put them under pressure", he said.
India were tottering at 19 for 3 in the 11th over and a recovery job was the need of the hour. There is no shortage of mutual respect between Nathan Lyon and Ravichandran Ashwin.
Harris and Khawaja were undone on 26 and 28 respectively by challenging, well-flighted deliveries but Marsh's sixth-consecutive single-figure score at Test level was more of a gift as he flashed at a wide ball only to drag it onto his stumps. Australian pacers were on target on day one.
More was glimpsed from the debutant Harris, who alongside Usman Khawaja seemed to be establishing a morning platform.
Quizzed about targeting India's lone spinner R Ashwin in this match, he replied the game-plan is going to be quite similar for even the Indian batsmen. Two came off Cummins; the first a pull shot that sailed for six and the other a proper cover drive that cleared the ropes as well.
Ashwin first struck before lunch.
Aaron Finch was bowled for a duck third ball by paceman Ishant Sharma and number four Shaun Marsh's awful run of form continued when he dragged spinner Ravichandran Ashwin onto his stumps for two after an excruciating 19-ball innings.
Fall of Wickets: 1/3, 2/15, 3/19, 4/41, 5/86, 6/127, 7/189, 8/210, 9/250.