The Giants revealed on Friday afternoon that the 23-year-old will undergo surgery on the lateral ligament in his knee and will miss the rest of the year.
The club's football manager Graeme Allan said: “While we obviously would have liked Tom to play the rest of the season, the medical advice is for him to undergo surgery now and the welfare of the player must always come first.
"We expect Tom to be ready to resume training for the pre-season later in the year."
Scully joins a growing list of players who will miss the rest of the season, including Jeremy Cameron (ankle), Tim Mohr (knee), Stephen Coniglio (broken thumb), Lachie Whitfield (shoulder and ankle), Aidan Corr (shoulder) and Nick Haynes (ankle).
In his third season for the Giants since crossing from the Demons at the end of 2011, Scully played 15 games and averaged nearly 20 disposals an outing.
Scully's place in Greater Western Sydney's squad has been taken by Tim Golds who will play just his fourth game of senior football.
Scully's former club Melbourne also suffered a withdrawal on Friday, with defender Jack Grimes (hamstring injury) coming out of the team to face the Brisbane Lions on Sunday. Veteran Daniel Cross replaces Grimes in the 25-man squad.
Magpie Paul Seedsman has been withdrawn from Collingwood's 25-man squad to play Port Adelaide on Sunday, with his place taken by Tom Langdon, who was initially dropped on Thursday night.
Seedsman has suffered an adductor injury.
