The matter will now be investigated by an Irish FA Disciplinary Committee.
Garrett scored in the 3-1 victory at Shamrock Park but the Irish FA will rule on whether the midfielder should have been on the pitch at all.
According to the IFA website, Garrett was to serve a one-match ban, effective from Monday, 24 October.
Portadown have insisted the suspension was to commence a week later.
It is understood Ards raised the matter of Garrett's eligibility before Saturday match.
The result at Shamrock Park was Portadown's fourth win of season, meaning they have wiped out the 12-point deduction imposed before the start of the season.
They are now on zero points - just five behind one-from-bottom Carrick Rangers.
The prospect of them having to facing another disciplinary hearing is the last thing Ports fans will want to hear.
If found guilty of playing a suspended player, Portadown's win could be changed to a 3-0 defeat.
Portadown's temporary manager Vinny Arkins said he sought clarification on whether Garrett was available for selection.
"I spoke to the club briefly before the game, regarding the issue of is the player suspended," said Arkins.
"I was told that he was cleared to play and that the suspension wouldn't kick in until the following Monday after it was received.
"So as far as I'm concerned, he was cleared to play.
"Ards did indicate it before the game, but they obviously know more than we do and they are obviously getting their information from someone other than us."
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The Northern Ireland Football League has formally raised the issue of Robert Garrett playing in Portadown's win over Ards on Saturday while suspended.