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Pucovski landed heavily in the field when diving to make a save on the final day and later went for scans, which coach Justin Langer revealed yesterday he was already due to have to check on another issue.
He travelled to Brisbane with the rest of the squad but did not train in the two days leading up to the Test.
"I think there'll be some discussions around Will's recovery," Tim Paine said. "What that looks like I'm not sure at the moment."
For Harris, who has been preferred ahead of shifting Matthew Wade back to open, it will be his first Test since the 2019 Ashes when he came in midway through the series as a replacement for Cameron Bancroft but made just 58 runs in six innings.
Harris wasn't part of the original Test squad but was added following the injuries to Pucovski (concussion) and David Warner (groin) which ruled the pair out of the opening two matches. He was then retained when Joe Burns was dropped after the second Test in Melbourne.
Harris was Pucovski's opening partner for Victoria in the Sheffield Shield earlier this season and the pair shared a record-breaking stand of 486 against South Africa with Harris making 239. He followed that with scores of 71 and 45 against West Australia then made 35, 25 not out, 26 and 5 for Australia A in the two warm-up matches.
"Harry's just a no-fuss very good player," Paine said. "He's been working his backside off in our hub for a while now. He's had huge numbers in Sheffield Shield cricket and deserves this opportunity. He just goes about his business, brings a bit of comedy to our team and he's a relaxed character.
"He's certainly someone we like having in and around our group and someone we have full confidence in that if he gets in and gets a start tomorrow that he'll cash in and make the most of it."
Pucovski's shoulder injury is another tough blow for the 22-year-old who was finally able to make his much-anticipated Test debut at the SCG and hit a composed 62 in the first innings.
It also means that Australia will have used five opening batsmen during the four-match series against India. Burns and Wade were paired together for the opening two matches before Warner and Pucovski joined forces in Sydney.