Uncapped legspinner Adam Zampa replaces Lyon in the only change to a squad that lost the final ODI against India on Saturday. The hosts won that series 4-1.
"This squad remains largely unchanged after a fantastic series win against India," national selector Rod Marsh said in a statement. "We have selected Adam Zampa as the spinning option for this tour in place of Nathan Lyon.
"We want Nathan to use the New South Wales versus West Australia Sheffield Shield match in New Zealand as preparation for the test series and this will give us a chance to have a good look at Adam ahead of the ICC World T20."
Australia will play two tests in New Zealand at the conclusion of the ODI series.
Left-hander Khawaja has scored five centuries and three half-centuries in his last nine innings in test cricket and Australia's 'Big Bash League' Twenty20 tournament.
Khawaja, who was drafted into Australia's squad for the second and third match against India after opener David Warner went on paternity leave, has played only three ODIs, the last coming against West Indies in Perth nearly three years ago.
"He doesn't have to do any more," Marsh told reporters in Adelaide on Monday. "He's in red-hot form and it's just a shame we can't fit Usman in.
"We tried our hardest to work him into the side but we just couldn't find anyone to drop."
Squad: Steve Smith (captain), David Warner, George Bailey, Scott Boland, James Faulkner, Aaron Finch, John Hastings, Josh Hazlewood, Mitchell Marsh, Shaun Marsh, Glenn Maxwell, Kane Richardson, Matthew Wade, Adam Zampa
(Reporting by Sudipto Ganguly in Mumbai; editing by Peter Rutherford)
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