Khawaja suffered a hamstring strain in the second test against New Zealand last month and missed the final test in that series as well as the innings and 212-run victory over West Indies in Hobart.
The 28-year-old was included in a 13-man squad for the Boxing Day test in Melbourne but told by coach Darren Lehmann that he would have to prove his fitness in Australia's Big Bash League.
The Thunder will play only two matches before the second test and Khawaja has now been scratched from the first -- a derby with Sydney Sixers on Thursday.
"Cricket Australia have been working with Thunder medical staff on Usman's return to play criteria following his hamstring injury," said a statement on the Sydney Thunder website (www.sydneythunder.com.au).
"At this stage the plan is to have him return for the Thunder's second match against the Melbourne Stars at the MCG on Sunday. His participation will be confirmed later in the week."
Grasping his third opportunity in test cricket, Khawaja had laid a solid claim to the number three spot in the Australian batting line-up with centuries in the first two tests against New Zealand.
The stylish lefthander's potential return will give the Australian selectors a dilemma after Shaun Marsh came into the side for Khawaja and scored 182 in a world record partnership of 445 with Adam Voges against West Indies.
Lehmann has said all-rounder Mitchell Marsh is assured of his place in the side because of the potential for injury in the bowling unit, leaving space for only five specialist batsmen in the line-up.
The unbeaten 269 Adam Voges scored in Hobart means he will surely join David Warner and Steve Smith as an automatic pick, leaving Shaun Marsh, opener Joe Burns and Khawaja battling it out for the remaining two spots.
Burns has not impressed in his five innings since scoring a century against New Zealand in Brisbane last month but Lehmann has questioned whether Smith would want to use Shaun Marsh, who batted at number five against West Indies, as an opener.
Khawaja is widely considered the most likely batsman to nail down the tricky number three spot in the Australian line-up, making him a certainty to play if he can prove his fitness.
(Reporting by Nick Mulvenney; editing by Ian Ransom)
