He joins David Pocock and Scogtt Higginbotham among the Qantas Wallabies' long term injury victims this year.
"It's unfortunate that having completed the healing process from last year's injury that it has happened again. There are a wide course of options open to Pat, which will be considered once the rehabilitation has been completed," said Qantas Wallabies doctor Warren McDonald.
"The fracture that has partially opened up is expected to repair itself and strengthen. This does not mean that Pat will not be able to return to the rugby field and be able to feel comfortable taking contact.
"The specialist advice is that a return is viable pending the full recovery and strengthening of the neck. Only time can do that, but we will be monitoring it closely throughout the healing process.
"There is certainly no way that Pat will be returning to the game without a thorough assessment process to ensure he can have full confidence in the bone that has fractured."
The initial stage of the rehabilitation will involve McCabe again donning a neck brace for a minimum of six weeks, stabilising the injury, before further assessment is made. He joins the Lions' Paul O'Connell and team mates Digby Ioane in being ruled out of the series following the first Test.