Masoud Shojaie and Ehsan Hajsafi played for Panionios against Israel's Maccabi Tel Aviv a week ago in a Europa League match.
Iran's Football Federation last week strongly condemned their participation, but prominent football players and many ordinary Iranians have backed the two on social media, saying they had no choice but to take part in the game.
FIFA's statutes ban political interference in its affiliated national associations, which can be suspended if the rule is breached.
"We are currently monitoring the matter and will request additional information from the Iran Football Federation," said a FIFA spokesperson in an emailed statement to Reuters. "We have no further comment for the time being."
If a country's FA is suspended, it means both the national team and its clubs are barred from international competition.
Iran have already qualified for next year's World Cup, making it an especially delicate matter for FIFA.
FIFA statutes state that "each member association shall manage its affairs independently and without undue influence from third parties".
The decision to suspend Shojaie and Hajsafi had been announced by Iran's deputy sports minister Mohammad Reza Davarzani on state TV.
"Hajsafi and Shojaie have no place in Iran’s national football team anymore ... they crossed Iran's red line," he said.
The two played in the home leg of the fixture but refused to play in the away leg in Israel, despite facing "pressure" and "financial fines" from their club, the sports ministry said.
(Writing by Brian Homewood; Editing by Andrew Bolton)