Thereafter, the other opener Marcus Harris (26) and the in-form No.3 Khawaja struck a 45-run stand for the second wicket.
The partnership went on smoothly as both the batsmen looked at ease while facing the pace trio of Ishant, Jasprit Bumrah and Mohammed Shami.
But Harris' troubles of reading off-spinner Ravichandran Ashwin was evident from the time the tweaker came in to bowl before eventually falling to the same bowler after a decent start.
Earlier, Australia took just one ball to wrap up the visitors' innings for the overnight score of 250.
Pacer Josh Hazlewood got the last man Shami (6) caught behind on the very first ball to deny the visitors any addition to the overnight score.
Earlier on Thursday, India were reduced to 19/3 before centurion Cheteshwar Pujara's gritty 16th Test ton (123) anchored the innings to 250/9 at stumps.
Pujara, however fell to a brilliant run out on the last ball of the opening day.
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