Khawaja will join the squad in Brisbane and, at this stage, will remain for matches two and three of the five-game series, at the Gabba on January 15, and at the Melbourne Cricket Ground on January 17, Cricket Australia said.
National selector Rod Marsh said Warner would be welcomed back into the squad when circumstances allow.
"We wish both David and Candice (Warner's wife) well and look forward to welcoming David back into the squad when circumstances allow," Marsh said.
"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."
Khawaja's most recent innings was a 42-ball 62 for Sydney Thunder against the Melbourne Renegades on January 11 and that followed on from his scores of 144 and 56 against the West Indies in the Boxing Day Test of the Commonwealth Bank series.
And after recovering from that injury, his first innings back was a brilliant 109 from 70 balls for the Thunder against the Melbourne Stars at the MCG on 20 December.
Meanwhile, Victorian all-rounder John Hastings would join the squad in Brisbane to allow Mitchell Marsh extra rest at home in Perth before returning to the group for the third ODI in Melbourne on Sunday.
Australia began the five-match ODI series in style, scripting an easy five-wicket win over India at the WACA.
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