Australia was left reeling on Thursday as captain Pat Cummins (ankle) and Josh Hazlewood (side) were officially ruled out of the tournament beginning in Pakistan this month.
Cricket Australia said the pair were beginning an "extended period of rehabilitation", having missed the current Sri Lanka Test series to recover.
But there is no suggestion they will miss Australia's next Test match - the World Test Championship final against South Africa in June.
With Mitch Marsh (back) also out, Australia is set to decide between Steve Smith and Travis Head as replacement skipper for the two upcoming ODIs against Sri Lanka and subsequent Champions Trophy.
Pacemen Sean Abbott, Spencer Johnson and Ben Dwarshuis will join the Australian squad for the two ODIs in Colombo.
Any of the trio could be retained for the Champions Trophy, as could legspinner Tanveer Sangha, allrounder Cooper Connolly and batter Jake Fraser-McGurk - also called into the squad for the Sri Lanka ODIs.
Australia does not need to finalise the Champions Trophy squad until February 12, the same day they play the first match in Colombo.
"While (the injury situation is) disappointing, it does present a great opportunity for other players to perform for Australia in a world event," said chief selector George Bailey.
Stoinis announced his retirement earlier on Thursday.
The 35-year-old allrounder played 74 ODIs for Australia but had only been selected once since playing in the victorious 2023 World Cup campaign in India.
Stoinis was named in the preliminary squad for the Sri Lanka ODIs and the Champions Trophy campaign that begins against England on February 22.
He will instead retire from the format in order to focus on franchise and international Twenty20 cricket.
Stoinis remains a highly rated T20 player, most recently earning selection in the Big Bash League's team of the tournament for helping the Melbourne Stars back to the finals.
He is currently playing for Durban's Super Giants in the SA20 competition.
"This wasn't an easy decision, but I believe it's the right time for me to step away from ODIs and fully focus on the next chapter of my career," Stoinis said.
"I'll be cheering the boys on in Pakistan."
Stoinis played his last ODI against Pakistan last November and retires with a batting average of 26.69, including an unbeaten 146 against New Zealand in 2017.
He took 48 ODI wickets at an average of 43.12.
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