Clarke appeared to have injured his right hamstring during his 46-ball innings.
He consulted team physiotherapist Alex Kountouris and immediately left the ground.
Cricket Australia confirmed Clarke had suffered a right hamstring injury that was being assessed by medical staff.
The skipper had slid down the order to bat at No6, behind Matthew Wade, and blasted five fours and a six as he looked for an opportunity to declare.
He was hit on the left leg during his first innings and required attention but hobbled on the make 74. He took his place in the field, standing at slip, but his movement was clearly limited.
Clarke's is the second injury Australia have suffered in the first test after swing bowler Ben Hilfenhaus broke down with a side strain on day three.
Hilfenhaus took his place at the crease but was out for a duck.
The pair add to a long list of injured Australian players, including James Pattinson (side), Patrick Cummins (back), Ryan Harris (shoulder), Josh Hazlewood (foot) and John Hastings (back).
- AAP