Canberra United will appeal a decision to have a 2-1 win over Sydney FC changed into a 3-0 loss after the club was found guilty of an unauthorised substitution last month.

In a move that sent Sydney FC to the top of the ladder and could have ramifications for the A-League Women finals, the Australian Professional Leagues confirmed the verdict on Monday and stripped three points from Canberra and gave the victory to Sydney along with a 3-0 win.

It’s a significant setback for Canberra who have fallen a game behind fourth-placed Melbourne Victory in their pursuit of a finals spot.

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The APL ruled an unauthorised substitution made in the 93rd minute of Canberra’s 2-1 victory over Sydney FC on February 11 violated competition rules.

A-Leagues commissioner Greg O’Rourke said Canberra had used all three of its available substitution windows when it made the change in the dying moments of the game.

Under competition rules, a team can only make a substitution in an additional window if it is to replace a concussed player.

“The final substitute was made at a time in the game when Canberra had already used all available windows under our regulations,” O’Rourke said.

“While it is unfortunate, the league must ensure its regulations are upheld.”

Canberra United chief executive Ivan Slavich said it was “extremely disappointing” to learn of the APL decision.

“We believe that we have not committed any violation of matchday regulations because of advice we received from the match officials during the fixture,” Slavich said.

“The club will be appealing the decision.”

United said it would make no further comment on the matter until the appeal was heard.

The APL confirmed the goals scored in the clash would still count towards individual awards, and Julie Dolan Medal votes from the match would remain valid.