The country's side was barred from playing a qualifier against Jordan before kick-off because their full-body strip included a head scarf.
In order to comply with the Islamic dress code - mandatory in Iran - female footballers play in full tracksuits and headcoverings that conceal their hair.
Fifa said Iranian officials were "informed thoroughly" before the match that the hijab scarf covering a women's neck is banned for safety reasons.
Iran's soccer association has said it will complain about the Fifa delegate from Bahrain who ordered the match abandoned.
Jordanian officials accepted the rule and decided not to select a number of players, Fifa said.
Farideh Shojaei, head of women's affairs at Iran's football federation, said Iran had made corrections to their kits beforehand after a Fifa ban last year.
Due to an automatic 3-0 defeat in the unplayed qualifier against Jordan, Iran's participation in London next year looks unlikely.
Mr Shojaei said: "We played the next round and were not prevented from doing so, and they didn't find anything wrong.
"That meant that there are no obstacles in our path, and that we could participate in the Olympics."
Mr Shojaei said that Iran's football federation chief Ali Kafashian "took it to Fifa and showed it to Mr Sepp Blatter" to prove they were not in breach of conduct.
"In reality, this kit is neither religious, nor political, nor will it lead to harm a player," Mr Shojaei added.
Fifa banned the hijab in 2007 and has extended the safety rule to include neck warmers.