Buhagiar looked set for a breakout season after scoring four goals in four FFA Cup games helping the harbour-siders to their third straight cup final.
The 20-year old, who left Central Coast Mariners for a two-year deal with Sydney, injured his right knee during a routine training game on Sunday.
He'll now miss the FFA Cup decider on October 30 and months of the new season.
"It's a blow for me being this close to starting the season but I’m determined to stay positive and do all of the right things to make a full recovery,” the Umina-based attacker said.
"I’ve had a lot of support from the boys and the staff, a few of whom have been through similar injuries and their help and positive words will be of enormous encouragement for me over the next few months.
“It’s a long road but I am looking forward to the journey and being back playing as soon as possible.”
Coach Steve Corica expressed his disappointment for the Olyroos striker but backed him to return and go onto big things.
"Trent is a fantastic young player and has been great for us since coming in, so to lose him is tough for both him and the club,” Corica said.
“He is a good person, with excellent character and will return an even better player having gone through this experience.
“We are fortunate that we have some great depth in our squad with Alex Brosque, Adam Le Fondre, Milos Ninkovic, Siem de Jong, Danny de Silva and Charles Lokoli N’goy all able to fill the void.
“However, we still have room to bring in another player and the fact we still have an international spot available is a bonus for us.”