The Englishman suffered a hamstring tear while scoring a goal in Saturday's 4-0 elimination final win over Macarthur.
The former Nottingham Forest star has arguably been the form player of the ALM this season and has been integral to the way Sydney play under Ufuk Talay.
The side host Central Coast Mariners in the first game of a two-legged semi-final tie on Friday.
"Unfortunately he's looking at quite a few weeks of rehabilitation, so (he'll) will miss the rest of the season," Talay said.
"It's a blow as Joe has had a fantastic year, but we've got great strength in depth, and players who have already shown they have what it takes to step in and perform in the big games.
"Now is the perfect opportunity for them to do that again."
In more positive news, Sydney captain Luke Brattan is an outside chance of facing the Mariners.
The veteran midfielder failed to finish the Macarthur win with an ankle injury, but Talay is keeping upbeat.
"We are taking it day by day with Luke, but the good news is there is no fracture," Talay said.
"The rest has been good for him and the ankle is improving every day.
"If he continues improving at the current rate then I am optimistic he will be good to go on Friday night."
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