Deputy Sports Minister Mohammad Reza Davarzani announced on Thursday that the Panionios pair would no longer be allowed to pull on the Iran shirt, following their appearance against Maccabi in the Europa League third qualifying round second leg in Greece earlier this month.
"Shojaei (r) and Haji Safi (l) have no place in Iran's national football team any more because they crossed the country's red line," Davarzani told state television.
"They have a financial contract with a club to be paid and play for that team, but to play with the representative of a loathsome regime... this is not acceptable for Iranian people."
Safi, who had a brief spell at FSV Frankfurt, and Shojaei had refused to play in the away leg in Israel despite facing "pressure" and "financial fines" from their club, the sports ministry said.
However, they did play in the return, which their side lost 0-1, to go out 2-0 on aggregate. The players have been backed by several renowned Iranian players both past and present including Ali Karimi and Mehdi Taremi.
Iran believes any dealing with Israel, including facing its players in sports, means recognising the Jewish state and betraying the Palestinian cause. "This is an illegitimate regime which we don't recognise," foreign ministry spokesman Bahram Ghasemi said.
Ghasemi's Israeli counterparts inevitably felt differently: "Well done to Masoud Shojaei and Ehsan Haji Safi who broke the taboo of not playing in matches against Israeli athletes," it said on its @IsraelPersian twitter account.
mp (AP, dpa)