Justin Langer clashed with match referee David Boon before a controversial concussion substitution allowed Yuzvendra Chahal to spin India to victory in the opening Twenty20 international.
In a dramatic match at Canberra's Manuka Oval, Australia fell 11 runs short of India's 7-161, with an injury to captain Aaron Finch adding to the pain.
Australia's chase stumbled after an 56-run opening stand between Finch and D'Arcy Short, with Chalal taking 3-25 to be named man of the match.
After starting the game on the bench, Chalal was brought in to the match as a concussion replacement for Ravindra Jadeja at the change of innings.
Jadeja top edged a Mitchell Starc bouncer into his helmet while batting in the final over of India's innings, but did not receive an on-field assessment.
Under the ICC's rules, a doctor does not have to come on to the field immediately but would have had to at the end of the over had the innings not concluded.
India captain Virat Kohli said Jadeja was dizzy at the time, and remained dizzy at match end.
Complicating the matter was that Jadeja had suffered an apparent hamstring injury in the previous over, and was clearly struggling to run during his unbeaten 44 from 23 balls.
Australia's main question, however, surrounded whether Chalal is a like-for-like replacement, given that he is a legspinner who bats No.11 and Jadeja is a finger-spinning allrounder.
Langer could be seen in a heated discussion with match referee David Boon in the innings break, as Jadeja was replaced by Chahal.
"It has nothing to do with his hammy. I would like to look into whether it's a like-for-like decision," Australia's allrounder Moises Henriques said.
"The like-for-like is one is an allrounder and a gun fielder, and the other one is an out-and-out bowler who bats No.11."
Chalal then claimed the key first two wickets of Aaron Finch and Steve Smith, before also removing Matt Wade late to open up Australia's lower order.
The legspinner had Finch caught on the long-on boundary to a great diving catch, while Smith and Wade both fell on the sweep.
Finch had earlier looked dangerous for Australia, flying to 35 off 26 balls and hitting one big six off his pads off Mohammed Shami.
But his glute remained a concern throughout.
He required attention during the innings, after he was hurt going down to field a ball at mid-off early in the game.
Australia have already rested Pat Cummins from the series, while Alex Carey was not selected on Friday but could return to open if Finch is ruled out.
Otherwise, Wade was vice-captain on Friday night while Steve Smith could loom as an option alongside Josh Hazlewood, Glenn Maxwell or Henriques.
"It was a bit of a hip or glute (problem)," Finch said.
"We'll wait and see after the game. It progressively got worse during the game, I am sure I will get a scan tomorrow and see how we go."
Earlier, Henriques produced the best bowling of his international career, claiming 3-22 on a wicket he used to his advantage.
His scalps included KL Rahul for 52 and Samson on 23, both caught in the deep on balls that held up slightly.
Mitchell Starc had the best night of his summer with 2-34, copping some tap late but bowling Shikhar Dhawan with one that swung away early.
Australian Associated Press
