Clarke pulled up sharply while fielding and left the field with the team physio, looking in a bad way with a right hamstring injury.
The Australian captain hobbled from the ground amid initial fears he would not be fit to lead his country in the second Test, getting underway in Brisbane on Wednesday.
A team spokesperson said Clarke had left the ground for scans to assess the injury. He appeared to have difficulty getting into the car that took him to the hospital.
Clarke suffered a recurrence of his long-term back injury while batting on Tuesday’s opening day which forced him to retire hurt.
He had injections to soothe spasms in his back and returned to the crease the next day to complete a century.
Clarke’s latest setback continued Australia’s frustration to push on for victory on the final day of the first Adelaide Test.
The Australians grabbed two wickets before lunch but were being resisted by opener Murali Vijay and skipper Virat Kohli, who batted through the entire middle session in an unbroken 148-run stand.
Faced with a 364 winning target off a minimum 98 overs after Australia declared on their overnight score of 290 for five, the tourists were 205 for two at tea.
Vijay was unbeaten on 85 with Kohli not out 82 and doing it comfortably.
No team has scored more than 315 to win a Test match at the Adelaide Oval since Australia overhauled England at the ground in 1902.
In hot sunny conditions, the Indians lost the wickets of Shikhar Dhawan and Cheteshwar Pujara in the extended morning session.
Dhawan appeared to get a bad call by umpire Ian Gould when he was given out caught behind off a Mitchell Johnson bouncer for nine in the day’s fifth over.
Replays indicated that the ball came off Dhawan’s shoulder and not glove as wicketkeeper Brad Haddin took an athletic catch down the leg-side.
Vijay survived a big shout on 24 for leg before wicket going back on his stumps off Lyon.
Umpire Marais Erasmus turned down Lyon’s vociferous appeal and replays showed the ball would have hit the stumps.
Pujara was done by one that Lyon straightened and he edged to Haddin for 21 in the 20th over leaving the tourists at 57 for two. – AFP