Messam had been named earlier on Thursday to start the match at blindside flanker but was a late withdrawal from the team as they finalised their preparations before flying to Australia.
"Gutted to miss on pulling on the black jersey for this weekend," Messam said on his official Twitter account. "Time to ice up and rest up and next week is a new week."
Local media said Messam could be out for as long as three weeks. The All Blacks were en route to Australia and unavailable for immediate confirmation.
Steven Luatua would instead make the trip to Sydney after initially being released to play for Auckland in New Zealand's domestic provincial championship this weekend, the New Zealand Herald reported.