Former captain Ponting on Thursday said he would be calling time on his glittering 17-year career after this week's third Test against South Africa.
Left-handed batsman Khawaja, 25, who made his Test debut for the injured Ponting in the Ashes test in Sydney in January 2011, will lead the side in the only warm-up game for the visitors before the three-test series kicks off in Hobart on December 14.
The Pakistan-born batsman averages 39 from six Test matches and is a contender for the number four batting spot in the Australian team, currently held by Ponting.
"It is a talented team that has an ideal mix of youth and experience," national selector John Inverarity said.
"Usman Khawaja has been nominated as captain. He, Glenn Maxwell, Alex Doolan and Scott Henry have been released from their BBL (Big Bash League) franchises to take this opportunity to further their experience in the longer form of the game.
"They are players who have shown some excellent form in recent months and will be looking to enhance their claims for higher honours."
Sri Lanka will also play five ODIs and two Twenty20 internationals during the two-month tour.
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