The 31-year-old hooker sustained the injury when making a tackle in the first minute of Saturday's 50-23 demolition of Les Bleus in Brisbane, ending his first test as captain after just three minutes.
"The whole year is gone ... he's obviously shattered," McKenzie told local reporters on Sunday.
"It leaves a bit of a void because we had put a lot of things in the pipeline."
The 92-cap veteran had scans after the match at Lang Park, which revealed torn anterior cruciate and medial ligaments and was told he would need a reconstruction.
"I'm going to need some surgery to repair my ACL/MCL," Moore said on his Twitter account on Sunday. "Will get it fixed up and look to go again."
The Wallabies captaincy is fast becoming the most unwanted job in world rugby.
Moore's injury follows the season-ending injuries in 2012 that afflicted James Horwill (hamstring), David Pocock (knee) and Will Genia (knee), who were all appointed to the role by former coach Robbie Deans.
Moore was also McKenzie's third captain in quick succession after he dumped Horwill from the role on their season-ending tour of Europe last year and replaced him with loose forward Ben Mowen.
Mowen, however, was not considered for the squad this season given his impending departure from Australian rugby following the Super Rugby season.
McKenzie named backline stalwart Adam Ashley-Cooper and openside flanker Michael Hooper as vice-captains before the series.
Hooper is likely to take the reins going forward after he took over the captaincy when Moore left the field on Saturday.
Tatafu Polota-Nau is likely to be promoted to starting hooker for the second test in Melbourne on Saturday.
In a double-blow for the Wallabies, lock Sam Carter, who made his test debut against France, will also miss the rest of the series with a high ankle strain, McKenzie confirmed.
