The decision by both A-League clubs to accept the sanction means they face the loss of three competition points if another incident of "significant magnitude" occurs this season.
The FFA decision stemmed from ugly street clashes between Victory and Wanderers fans in Melbourne on December 28 prior to the side's match at AAMI Park, in which eight people were reportedly hospitalised and two arrested.
FFA boss David Gallop said the game's governing body was working with both clubs to ensure such scenes were not repeated.
"We respect both clubs for their stance on the difficult issue of identifying the small number of troublemakers who tarnish the overwhelming majority of true football fans," Gallop said in a statement.
"FFA and the clubs' response is designed to galvanise the football community against the scourge of anti-social behaviour.
"The great majority of fans who create such a wonderful atmosphere at the A-League should get to the matches and enjoy themselves this weekend.
"Those who cause trouble are on notice that enough is enough."
Wanderers chairman Lyall Gorman said: "As a club we have always maintained a policy of zero tolerance in relation to anti-social behaviour.
"Agreeing not to contest the sanction demonstrates the club's commitment to a unified and whole of game approach to ensure a safe environment at all times for our members and all genuine supporters of our club and the game."
The two sides meet at the same venue again on Tuesday and the FFA said it had reviewed security and ticketing arrangements for the fixture in consultation with police.
Victory chief executive Ian Robson said they were supportive of the FFA's approach.
"We have opted not to contest the sanction on the basis that we are fully supportive of FFAs stance to adopt a zero tolerance approach to anti-social behaviour," he said.
"Further to this, the FFA has proposed new measures, in conjunction with other stakeholders, to ensure we deliver a safe and enjoyable environment for our members and fans, which will be continually monitored for the remainder of the season.
"The FFA has also demonstrated their ongoing commitment to working with all A-League clubs and relevant stakeholders, to ensure these standards are reviewed and enhanced to deliver consistency across the league for subsequent seasons; therefore fostering the continued growth in the popularity of our sport."