Warner scored five runs in Australia's innings as the hosts registered a five-wicket victory in the opening clash of the five-match series in Perth on Tuesday but will miss matches two and three in Brisbane and Melbourne.
Khawaja, who recently made a successful return to test cricket in the home series against New Zealand and West Indies, will replace his fellow left-hander, whose wife Candice is expecting their second child.
"Usman has been in fantastic form this season and was unlucky to miss out on a place in our squad ... in the first place," chief selector Rod Marsh said in a news release.
"This call-up is a reward for that form and it is great to have someone of his quality to step into the squad in David's absence.
"We wish both David and Candice well and look forward to welcoming David back into the squad when circumstances allow."
Khawaja has played only three one-day internationals, the last coming against West Indies in Perth nearly three years ago.
The 29-year-old hopes he can make the opportunity count if he does get one.
"The hunger is to play as many forms of the game as possible," he told reporters at Sydney airport. "I've made it clear that I've always wanted to play one-dayers.
"But sometimes it's about timing. If I'm going to get my opportunity, I don't know, but when I do get it hopefully I can take it and be more than just a test cricketer.
"At this moment I'm really happy with how I'm hitting the white ball."
The second match against India takes place in Brisbane on Friday with the teams meeting at the Melbourne Cricket Ground on Sunday before the series concludes with fixtures in Canberra and Sydney.
(Reporting by Nick Mulvenney and Sudipto Ganguly in Mumbai; Editing by Andrew Both)
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