Hughes and Khawaja, who both played in Australia's 3-0 defeat in the first Ashes series of the year in England, will instead play Sheffield Shield matches for their states.
Callum Ferguson, though, gets another chance to face the tourists after wet weather limited his opportunity to impress for Australia A in Hobart last week.
"Callum Ferguson didn't get the depth of international exposure we hoped to give him through his Australia A selection," Cricket Australia's Pat Howard said in a news release.
"We felt it made sense to select him in the next tour match against England.
"In light of Callum's selection, Phil Hughes, who has played a lot of international cricket in recent months, will remain with South Australia for its next Shield match."
Australia name their squad for the opening test on Tuesday in Brisbane, where the series gets underway at the Gabba on Nov. 21.
Invitational XI: Ed Cowan, Aaron Finch, Callum Ferguson, Adam Voges, Ben Rohrer, Ryan Carters, Peter Nevill (captain), Stephen O'Keefe, Josh Lalor, Chris Tremain, Nic Bills.