Team officials said Clarke, 27, should recover in time for the Test starting on Thursday, but his absence from practice is not what the tourists needed before the four-match series.
All-rounder Shane Watson was forced to sit out of the tour opener in Hyderabad last week with a chest infection, missing valuable match practice.
Australia need a fit Clarke both as an accomplished middle-order batsman and left-arm slow bowler in the absence of better spin options.
Clarke said last week he was looking to make a positive impact in the Bangalore Test, just as he had done on the previous tour four years ago.
"I have had success before in Bangalore and hopefully I can repeat that this time too," Clarke said in Hyderabad.
It was at the same Chinnaswamy stadium in Bangalore in 2004 that Clarke made a memorable Test debut aged 23, scoring 151 to lead Australia to a 217-run win.
Clarke is now one of only four Aussie players, alongside skipper Ricky Ponting, Matthew Hayden and Simon Katich, to have experienced a Test match atmosphere in India before.
Clarke, nicknamed 'Pup' by team-mates on the previous Indian tour, is not only Ponting's deputy this time, but one of the key Australian batsmen who is comfortable playing spin.
He has racked up 2,212 runs in his 35-Test career.