Two balls into his first over, Stoinis left the field for what turned out to be a side strain.
After a few scans were taken, the reports were a low-grade side strain.
A cricket Australia spokesman said the injury would be monitored carefully.
With a minimal gap between games, the recovery time is minimal as Stoinis is likely to miss the second ODI.
Marcus was out for a duck as Australia made 374 to beat India.
The side strain is not Stoinis’s first, as he has previously been injured in the 2019 World Cup.
The one in the 2019 World Cup may have been more severe as he has gotten a lower grade strain this time.
While he did not do much with the bat, he bowled well in Australia’s defense.
He conceded 25 runs in 6.2 overs, significant figures in a match where almost every bowler went out of the park.
He continued his golden run with the ball after having a right IPL, and, unfortunately, his injury has halted his progress.
In Stoinis’s absence, Australia may have to hand Cameron Green his ODI debut.
Green has been earmarked as a talented bowler and is also in the test squad.
He can also bat decently and maybe a decent replacement for Stoinis.
The squad also has Moises Henriques, who is on the team for the first time since 2017.
Henriques is a talented all-rounder and quite similar to Marcus Stoinis on paper.
His presence allows Australia to field a like for like replacement for Marcus Stoinis.
Other options are Sean Abbott, a good bowler and can bat but are more of a bowling all-rounder.
Ashton Agar is another all-rounder who can be considered, and with his inclusion, the spin bowling may have more depth as well.
Having Agar would guarantee another front-line spinner while the side already has Adam Zampa and Glenn Maxwell.
It would mean the side has a wrist spinner, left-arm-spinner, and off-spinner on the side.