The veteran spinner will miss the rest of the Ashes and be on the sidelines for months due to the injury he suffered in Adelaide on Sunday.
Todd Murphy has been called into the 15-man squad as a replacement for Lyon as the Victorian prepares to play his first Test in Australia.
Working in Lyon's favour is Australia's next Test after this summer isn't due until August, giving him plenty of time to recover for that two-match Top End series against Bangladesh.
After spending time in hospital post-operation, the 38-year-old will join the Australia squad in Melbourne to support them for the Boxing Day Test.
"He's pretty shattered," McDonald said when asked about Lyon's injury.
"Any time you're facing a long time out - and we saw that on the back of the Lord's Test match (in 2023) as well.
"He's a huge part of what we do.
"He's facing a long recovery time frame, so I'll leave that up to the medical team, but all I know is it'll be pretty long-ish (recovery)."
Although 2026 will be a relatively quiet year for the Test team, the 12 months that follows is set to be the busiest ever for Australia.
McDonald's team will tour India in January 2027, return for the 150th anniversary Test at the MCG against England in March, before preparing for an away Ashes in the middle of the year.
Lyon, who in Adelaide surpassed Glenn McGrath as Australia's second-highest Test wicket-taker, has dominated in recent tours of Asia.
"It's going to be a hard period for him to get back to where he was," McDonald said.
"But he still wants to do it, and that's the main thing.
"In Adelaide, it was probably the best I'd seen him bowl for a little while.
"He'll get through this rehab and then look forward to what it looks like."
Lyon has enjoyed an injury-free run through most of his Test career, with the other setback of note being a torn calf in the 2023 Ashes.
Murphy replaced fellow offspinner Lyon in Australia's XI after that 2023 setback at Lord's.
The 25-year-old has played seven Tests - all outside of Australia - famously taking seven wickets on debut in 2023 against India in Nagpur.
Murphy last played for Australia in January during a thumping win against Sri Lanka in Galle.
As expected, captain Pat Cummins will sit out the rest of the Ashes as he protects his body following a serious back injury this year.
Cummins conceded after the win in Adelaide he was unlikely to feature at the MCG.
Steve Smith is expected to be fit after a vertigo episode forced him to miss the third Test, with the star batter to again captain Australia in Cummins' absence.
Western Australia quick Jhye Richardson is in contention to play his first Test in more than four years after also being recalled to the squad.
Richardson has endured a torturous run with injury, but has made a flawless return to cricket in recent weeks.
Australia will need to replace Cummins so Richardson will be battling it out with Brendan Doggett and Michael Neser for a spot in the XI.
A decision must be made on who makes way for Smith, with Usman Khawaja and Josh Inglis likely vying for one spot.
Khawaja, who turned 39 last week, made valuable contributions of 82 and 40 when batting at No.4 in the series-clinching win at Adelaide Oval.
The veteran left-hander's Test career seemed over before Smith was a late withdrawal on the morning of the match.
AUSTRALIA: Steve Smith (capt), Scott Boland, Alex Carey, Brendan Doggett, Cameron Green, Travis Head, Josh Inglis, Usman Khawaja, Marnus Labuschagne, Todd Murphy, Michael Neser, Jhye Richardson, Mitchell Starc, Jake Weatherald, Beau Webster.
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