Glory tried to appeal against the automatic one match ban claiming an obvious error had been made by the referee after they were given conflicting reasons for the second yellow during the New Year’s Eve match against Central Coast Mariners.
Glory claim they were repeatedly told on the night that Burns had been booked for entering the field of play without permission, but replays of the incident appear to contradict that.
The FFA later told the club the referee had shown Burns the second yellow on the advice of the fourth official for showing dissent to the fourth official.
"It is clear now that there had been a failure in the officiating process and communication between the referee and fourth official during the match," Glory said in a statement today.
"Perth Glory is extremely disappointed to have learnt that the referee issued the second yellow card, at such an important moment in the match, without fully understanding why he was actually issuing the second yellow card, without fully understanding the facts of the situation and without exercising any of his own judgement to determine if the second yellow card was actually the appropriate course of action to take.
"Following the final whistle the referee advised several players from both teams, as well as Perth Glory's interim head coach, Kenny Lowe, that the second yellow card had been shown to Jacob Burns for 'entering the field of play without permission'.
"The referee advised that this was consistent with the yellow card issued to Mariners’ defender, Marcel Seip, earlier in the match. 
'Television footage clearly shows Jacob Burns did not enter the field of play and as such the basis for the referee issuing the second yellow card was incorrect.
"Perth Glory argued that an obvious mistake had been made and the Referee had not performed his duties correctly."
"Perth Glory is unhappy that the process followed by the referee, to act on the advice of the fourth official without clarifying the precise reasoning, was flawed. 
"The FFA has advised that this will now be addressed with the match officials to ensure that something like this cannot occur again in the future.
"Perth Glory hopes that the FFA will act effectively to ensure that such incidents do not happen again in the Hyundai A-League."
The statement added: "Perth Glory does not condone the alleged dissent directed to the fourth official."
Perth Glory owner Tony Sage branded the confusion a farce and demanded an imporvement in the A-League's refereeing.
“All owners are concerned about the standard of refereeing in the Hyundai A-League and as a group we have consistently brought this issue to the attention of the FFA,” he said.
“The post-match explanations we received when seeking clarification on the Second Yellow card were farcical given the professionalism that we expect from all involved in the A-League."