Question: Is it allowed to have successful entry into Iran or visa application with Israeli stamp in your passport?
Answer: Due to the rules dominating over Iran, entry to Iran will be refused for citizens of Israel and travelers with any evidence of visiting Israel. Israel is the only county included in this rule and other countries even America are excluded.
You should change your passport and then apply for your visa in these three ways:
1. Fill in the visa form on http://www.uppersia.com/Iran-Visa-Box/iran-visa-authorization-reference-number-invitation-application-form.html, it takes about 10-15 working days to get your reference number and two working days to collect your visa at the embassy by direct referral or one working week by posting the docs to the embassy. You can pay the visa fee in cash in Iran.
2. Fly to Iran and get a 14-day on arrival visa at the airport. This kind of visa is issued for 98 nationalities excluding USA, England, Canada, Colombia, Pakistan, Afghanistan, Iraq, Jordan, Bangladesh, and Somalia. If your nationality is among the countries authorized to get it, you can easily collect you visa against offering your passport, a passport-size photo and about $50 to the staff at the airport. There is no need to fill in any form beforehand.
3. Refer to the Iranian embassy in your country and ask for a visa to be issued for you. Usually this way takes longer time about 30 days.