The injury will rule him out of involvement in the 2019 Asian Cup with Australia as well as the Terriers’ December fixtures.
The 28-year-old suffered a tear to the Medial Collateral Ligament (MCL) in his right knee in last Saturday’s Premier League game at Arsenal.
After consulting a specialist on Tuesday, he has been ruled out until February.
Mooy said: “I’m gutted to be missing an important time for Club and Country.
“We’ve got a lot of fixtures over the Christmas period at Huddersfield Town, but I back the team to continue our good performances and get the results that we’re targeting.
“I’m also sad that this injury will rule me out of the Asian Cup. I’d like to wish the Socceroos all the best as they head to the UAE; I’ll be supporting them from afar.
“The hard work on my recovery has already started and I’m looking forward to being back out on the pitch.”
In a further blow, scans have also confirmed that club captain Tommy Smith suffered a tear in his right hamstring at the Emirates Stadium on Saturday. His projected return to fitness is in January 2019.
“The news on both Aaron and Tommy is not something we wanted, but injuries are part of football; we have to deal with it, manage it and carry on into this important December period.
“Aaron and Tommy are both strong characters and will work very hard in their recovery. We look forward to having them back.
“For now, this creates opportunities for others. I’ve said all along that we will need everyone in the squad to contribute and now we should see the benefits of having such a competitive squad.”
Terence Kongolo (knee) and Jonathan Hogg (groin) both picked up knocks in the game and are being monitored day-to-day.
Midfielder Abdelhamid Sabiri has undergone a successful operation to repair the broken collarbone he sustained in the previous Premier League fixture at AFC Bournemouth and, like Mooy, is projected to return to full fitness in February 2019.