Abbas was on the scoresheet as the Sky Blues consolidated their spot in the top six with a 3-1 victory over arch rivals the Western Sydney Wanderers in front of a capacity crowd at Allianz Stadium.
However, the sixth instalment of the Sydney Derby was marred by claims Abbas was vilified by a Wanderers opponent on the basis of his religion or culture.
The Iraqi-born player was visibly upset following the final whistle, with team-mates Sasa Ognenovski and Hagi Gligor forced to restrain the 27-year-old.
And the FFA released a statement on Sunday confirming an official complaint is set to be made.
"Football Federation Australia (FFA) has received advice from Sydney FC that a formal complaint from Ali Abbas will be lodged in relation to an alleged incident during the Hyundai A-League Round 22 match between Sydney FC and Western Sydney Wanderers last night.
"Such complaints are dealt with under FFA’s National Member Protection Policy. Upon receipt of the formal complaint, FFA will instigate an investigation of the incident. The resolution process may include mediation or referral to a Disciplinary Tribunal.
"Under the National Member Protection Policy, the process is conducted confidentially and therefore FFA will make no comment about the allegation or the investigation."
Sydney FC CEO Tony Pignanta added: "We will be undergoing due process with FFA.
"We ask that the privacy of Ali Abbas is respected at this time and no further comment will be made while the complaint procedure takes it course."
In what was meant to be a celebratory night for the Sky Blues turned sour, with Abbas voicing his displeasure in an interview with Fox Sports post-match.
"We are not here to attack religion or culture; we are here to play football," Abbas told reporter Tom Chadwick.
"I come from a different country, I respect everyone here. I should get it back. If I don't get it back, I'm going to attack. That's what happened.
"If people attack religion, if people attack culture - I'm against that. We need to stop that."
The incident comes a week after the A-League's 'Erase Racism Round', an initiative to combat the fight against racism.
