The fans were forced to leave the match in Grenoble after being approached by Fifa steward
Fifa says it was wrong to remove fans from a Women's World Cup match for wearing T-shirts calling for Iranian women to be let into football stadiums.
Two fans were removed during Canada's 2-0 win over New Zealand on Saturday because their T-shirts carried slogans.
However, Fifa has now said the message was "social, not political" so not against its rules.
The governing body added it "will do its best to ensure similar situations do not occur at future matches".
The Open Stadiums movement has been campaigning for women to be allowed access to men's sporting events in Iran after a 40-year ban.
In March 2018, 35 women were detained for trying to watch a football match in Tehran, but in October a select number of women were allowed access to a friendly match between Iran and Bolivia.
Fifa has been working with Iran to try to end the ban.
The incident in Grenoble last Saturday was witnessed by Australian fan Petr Kuzmin, who said the couple wearing the T-shirts, which also had a message about hijabs - headscarves worn by some Muslim women - on the front, did not resist.
But Kuzmin said he was "incensed" by what he saw and described it as an "insane irony".
"The main message [on the T-shirts] was about allowing women access to stadiums and to have it censored like this seemed ridiculous," he told BBC Sport.
"I'm glad Fifa made the right decision to formulate the right response, even if it took three days, and I think it's a good sign that they are interested in promoting women's access to stadiums in Iran."
The steward's decision to remove the fans was the wrong one, Fifa now says
Fifa said in a statement it "believes that the message to allow women into football stadiums in Iran is a social, not political, matter and so the message on the front of the T-shirts worn by two fans is not against Fifa rules, which always need to be applied with a sense of proportion".
The world governing body added: "As such, in this specific case, the fans should not have been asked to remove their T-shirts or to leave the stadium by local security, even if there were other messages on the back of their T-shirts.
"Fifa will do its best to ensure that any similar situations do not occur at future matches during the competition."
-- Courtesy of BBC Sport