Club CEO Tony Pignata admitted the players were put off by the lack of their most vocal supporters.
"We really missed them, and speaking to some of the players they felt that as well," Pignata told AAP.
If Sydney FC players felt the silence then it must have been positively eerie for those in the red and black of Western Sydney.
So often a cacophony of drums, chants and colour, Pirtek Stadium's North Terrace was empty for the Wander previous home game against the Phoenix two weeks earlier.
"They [fans] have their grievance [but] we want them back as soon as possible. I'd love to see them behind the goals, filled to capacity, against the Victory next week," said Wanderers boss Tony Popovic.
Supporters initially staged walk-outs in round eight following the FFA's inaction over a NewsCorp report that named and shamed 198 banned supporters.
They were further angered by the lack of a transparent policy whereby fans could dispute match bans handed down by the FFA and a subsequent press conference by CEO David Gallop who urged fans to "use your energy from now on in a positive way".
Gallop has since apologised and said there would be a new process for contesting bans in place by February.
Wanderers CEO John Tsatsimas said he would like that process brought forward while fan groups have not made it clear if they'll continue to boycott games.
CENTRAL COAST MARINERS V MELBOURNE CITY
Crowd: 4514
Previous home game: 10,519
Lowest ever home crowd (Regular season): 4508, Feb 7, 2015 v Adelaide United
Highest ever home crowd (Regular season): 17,514 Dec 22, 2007 v Sydney FC
SYDNEY FC V NEWCASTLE JETS
Crowd: 9155
Previous home game: 9253
Lowest ever home crowd: 4012, Dec 1 2010 v Wellington Phoenix
Highest ever home crowd: 41,213 October 18, 2014 v Western Sydney Wanderers
WELLINGTON PHOENIX V MELBOURNE VICTORY
Crowd: 10,852 (QBE Stadium in Auckland)
Previous home game: 13,654
Lowest ever home crowd: 4025, Feb 27, 2013 v Newcastle Jets
Highest ever home crowd: 18,345, Nov 30 2007 v Adelaide United
WESTERN SYDNEY WANDERERS V BRISBANE ROAR
Crowd: 9680
Previous home game: 14,426
Lowest ever home crowd: 6755 Dec 9 2012 v Brisbane Roar
Highest ever home crowd: 19,484, Feb 28 2015 v Sydney FC
ADELAIDE UNITED V PERTH GLORY
Crowd: 6205
Previous home game: 10,048
Lowest ever home crowd: 5898, March 1, 2012 v Perth Glory
Highest ever home crowd: 16,504 October 18, 2013 v Melbourne Victory
- AAP