The Queensland captain is fit and healthy, but on Saturday he will watch his side’s clash with Victoria in Mackay from his home in Brisbane.
Queensland still have four Shield games before the first Test of the summer against Pakistan, beginning in Perth on December 14.
Australia, currently competing in the ODI World Cup in India, will play a five-game T20 series against the hosts, before returning home for a five-Test summer.
They will also play two Tests in New Zealand in February and March, and contest T20 series alongside those five-day clashes.
AAP understands all Australian squad members will be subject to the load management policy – which had not been flagged before Khawaja’s omission on Thursday – on a case-by-case basis.
The 36-year-old Khawaja has a relatively light schedule compared with some of his Test team-mates who frequent the world T20 circuit, but he will play for the Brisbane Heat in the BBL.
His omission is a nod to how crowded the modern-day cricketer’s calendar has become.
“Ideally you want your captain and best player to be there for every game, but we all know that, barring injury, he will be one of the first bats picked for the Pakistan series, so we understand the rationale behind the decision-making process,” Queensland coach Wade Seccombe said.
“Uzzie is philosophical about it. He’d be happy to play, but he will also benefit from a more measured build-up ahead of another big international schedule for Australia.
“He’s hitting them well, so we shouldn’t be too concerned on that front.”