The Welshman was forced off with a leg problem during the 16-15 loss in Melbourne as the Wallabies tied the three-Test series 1-1.
"I felt something in my [hamstring]," Warburton told Sky Sports News. "I've put some ice on it and the physios will assess it in 24 hours time. Fingers crossed."
The two teams will battle it out in the series decider in Sydney next Saturday.