Doherty was called into the limited overs squad after Nathan Hauritz suffered a dislocated shoulder during the third match of the current series against England in Hobart, placing him in severe doubt for the World Cup on the subcontinent.
However Doherty's own fitness now appears questionable after he complained of renewed back pain in training ahead of Wednesday's sixth match at the SCG.
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The problem had first emerged during the Australia Day match at Adelaide Oval, forcing Doherty to miss out in Brisbane, but he is yet to show signs of improvement and has now been ruled out of the remainder of the series.
"Xavier Doherty developed some back pain during the one-day game in Adelaide on Australia Day and did not train in Brisbane," said team physio Alex Kountouris.
"He attempted some light training yesterday in Sydney and his back was again painful.
"As such he is unavailable for the remaining two games of this series.
"His return to cricket will be determined by monitoring his recovery over the next week."
While the all-rounder Steve Smith has done a serviceable job as a limited overs spin bowler, Australia would be reluctant to go to India without one more option, though where they go in the absence of Doherty and Hauritz is questionable.
Sydney Test debutant Michael Beer may be in the frame, while Doherty's Tasmania teammate Jason Krejza has bowled well in limited overs cricket this summer, and took 12 wickets on his Test debut against India in Nagpur in 2008.
Victoria left-arm spinner Jon Holland toured India with the Australia one day side in 2009, though he did not play a match, while New South Wales slow man Steve O'Keefe has played at Twenty20 level for the national side.
More left field is the young South Australian off break bowler Nathan Lyon, 23, who has impressed many with his flight and pace variations during the current KFC Big Bash tournament.
Lyon, however, has yet to play at any other level for the state.
