Veteran seamer Peter Siddle was included in Australia's revamped 14-member squad for the three-match ODI series against India starting here on January 12.
Off-spinner Lyon had missed the ODI series against South Africa at home earlier in the season, while Khawaja too is making the ODI squad after almost two years.
Mitchell Marsh and keeper Alex Carey will be the two vice-captains in keeping with Cricket Australia's new policy after the ball-tampering saga.
The trio of Mitchell Starc, Josh Hazlewood and Pat Cummins, however, have been rested keeping the Test series against Sri Lanka in mind.
Batsmen Travis Head, Darcy Short and Chris Lynn have been left out owing to recent poor form in ODIs, while fast bowler Nathan Coulter-Nile has been rested owing to lower back issues.
Australia's selection panel chairman Trevor Hohns said the decision to revamp the squad was taken due to the team's poor show against South Africa and also keeping the World Cup in mind.
"With this in mind and the World Cup looming, we've selected players we feel provide us with the flexibility to play a variety of roles at different stages of a match," he said.
"The upcoming three-match series against India and the ODI tours of India and the UAE are important windows to put this into practice and to build a squad to help defend our World Cup title."
The other two matches of the three-ODI series will be played in Adelaide (on January 15) and Melbourne (January 18).
Squad: Aaron Finch (C), Usman Khawaja, Shaun Marsh, Peter Handscomb, Glenn Maxwell, Marcus Stoinis, Mitch Marsh, Alex Carey (WK), Jhye Richardson, Billy Stanlake, Jason Behrendorff, Peter Siddle, Nathan Lyon, Adam Zampa.
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