Masoud Shojaie and Ehsan Hajsafi played for Panionios against Israel's Maccabi Tel Aviv on August 3. Iran's Football Federation last week strongly condemned their participation.
Iran does not recognise the state of Israel.
"Hajsafi and Shojaie have no place in Iran’s national football team any more ... they crossed Iran's red line," Iran's deputy Sports Minister Mohammad Reza Davarzani said.
"Playing against the representative of a loathsome regime (Israel) ... is unacceptable for our nation.”
The two players 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.
Prominent football players and many ordinary Iranians have backed the two players on social media, saying they had no choice but to play the match.
But Iranian Football Federation officials said they should not have played “even if their contracts with the Greek team would have been terminated".
(Writing by Parisa Hafezi; editing by Andrew Roche)
