Rohit looked in good touch during his 44 off 74 balls but was dismissed trying to loft Lyon over mid-wicket.
The Indian opener was seen limping immediately after holing out to long on just before tea on the second day of the fourth and final Test at the Gabba.
Rohit spent his second consecutive day training at the Melbourne Cricket Ground on Friday.
"So how was your quarantine, my friend," chief coach Ravi Shastri was heard asking Rohit in a video posted by BCCI.
The Indian skipper lavished praise on the marauding Hardik Pandya's "raw talent".
Rohit will have to undergo a mandatory 14-day quarantine on arrival in Australia, which will rule him out of the first two Tests in Adelaide and Melbourne.
The opener is out of reckoning for the first two Tests against Australia, but can now be there for the last two games.
The Indian captain said he was kept in the dark about deputy Rohit Sharma's hamstring injury and believes the opener should have travelled to Australia to boost his chances of playing the Test series against Tim Paine's men.
The in-form Mayank Agarwal is likely to open with Shikhar Dhawan in Rohit's absence in the ODI series beginning Friday.
The two have been ruled out of the two Tests against Australia and are also doubtful for the remaining two after it was conveyed to the BCCI that the duo will require close to a month to be match fit.