Khawaja was recently dropped from the central contracts list after having not played for Australia since last year.
Khawaja, 33, most recently played for Australia during the summer last year, featuring at the 50-over World Cup as well as the Ashes in UK.
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The selectors decided not to retain him for the home season against Pakistan and New Zealand, where Khawaja's replacement, young Marnus Labuschagne cemented his position in Test middle-order and later made a good early impression in ODIs during tours to India and South Africa.
Khawaja was subsequently left out of the next annual central contracts list as well.
"I honestly think now he's going to find it difficult (to get back into the Australian team) and I feel for him," Ponting told ABC Grandstand.
"I've always felt he's a very good player and we probably never saw the absolute best of him at international cricket. We saw glimpses of it, and dribs and drabs, but not the consistently good player I thought he could have been for Australia."
However, that isn't to say there is no light at the end of the tunnel for Khawaja.
"One thing I know, you never write great players off," Ponting said. "He's got every opportunity once domestic cricket does start this summer, and all he can do is represent Queensland, get a truckload of runs under his belt and wait for another opportunity to come along."
"If it does I'm sure he wouldn't let anyone down if he gets a chance to play again," added the legend on Khawaja, who boasts of 2,887 runs in Tests and 1,554 runs in ODIs for Australia.
(Inputs from PTI)