Griffin crumpled to the ground after his right knee buckled at a boundary throw-in halfway trough the first term and was subbed out of the match before quarter-time.
It is another body blow to Fremantle's ruck stocks after Kepler Bradley ruptured his ACL against Richmond a fortnight ago.
Aaron Sandilands is still approximately six weeks away from returning after suffering a hamstring injury during the pre-season.
Fremantle's general manager of football operations Chris Bond said in a statement that a decision would be made in the next few days as to the timing of the surgery.
"Jon's been in great form and it's bitterly disappointing," Bond said.
"But knowing his character and professionalism, Jon will be doing everything that's required through his rehabilitation phase to be back playing footy next season."
Fremantle forward Matt de Boer spoke to the media at recovery on Sunday, prior to Griffin's scan, but said he had spoken with his teammate after the match.
"I spoke to him briefly last night. He's obviously very devastated," de Boer said.
"We're testing our depth."
If there was a positive to be found then the performance of third-gamer Jack Hannath in the ruck was it, according to de Boer.
"It's just great that anyone who comes in, we know that they're going to fulfil a role and their going to bring great effort.
"Jack's been really good and he'll have to step up again."
Zac Clarke is another who will come back into contention after recovering from a calf problem but Fremantle coach Ross Lyon hinted post-match that Clarke would not automatically return to the senior side.
If that were the case, Fremantle would go into their clash with Sydney Swans on ?Saturday with Hannath and Zac Dawson in the ruck against the reigning premiers.
