Individuals who showed dissent towards Tehran were harassed by government backers, while stadium security seized flags, T-shirts and other items expressing support for the protest movement.
Security guards prevented some fans from bringing in Persian pre-revolutionary flags to the match at the Ahmad Bin Ali Stadium.
Meanwhile, others carrying such flags had them ripped from their hands by pro-government Iran fans.
Insults were also shouted at people, wearing T-shirts with the slogan of the protest movement gripping the country: "Woman, Life, Freedom."
Unlike in their first match against England, the Iran players sang along to their national anthem before the match as some fans in the stadium wept, whistled and booed.
The national team has come under close scrutiny for any statements or gestures about the nationwide protests that have wracked Iran for weeks.
Shouting matches erupted in lines outside the stadium between fans screaming "Women, Life, Freedom" and others shouting back "The Islamic Republic!".
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Mobs of men surrounded three different women giving interviews about the protests to foreign media outside the stadium, disrupting broadcasts as they angrily chanted: "The Islamic Republic of Iran!"
Many female fans appeared shaken as Iranian government supporters shouted at them in Farsi and filmed them up close on their phones.
Following the conclusion of the game, which ended 2-0 to Iran, crowds of Iranian fans wildly waving national flags streamed out of the stadium.
They swarmed a group of protesters who held up photos of Mahsa Amini, the 22-year-old whose death in the custody of the morality police first unleashed the protests.
One 35-year-old woman named Maryam, who like other Iran fans declined to give her last name for fear of government reprisals, started to cry as a group of men surrounded her.
She had the words "Woman Life Freedom" painted on her face.
"I’m not here to fight with anyone, but people have been attacking me and calling me a terrorist," she told the Associated Press.
"All I’m here to say is that football doesn’t matter if people are getting killed in the streets."
Furious protesters in Iran have been venting their anger over social and political repression and the state-mandated headscarf, or hijab, for women.
The demonstrations have quickly grown into calls for the downfall of the Islamic Republic itself.
At least 419 people have been killed since the protests erupted, according to the monitoring group Human Rights Activists, in Iran.
The turmoil has overshadowed the start of Iran’s World Cup campaign, including the opening match against England on Monday.
Iran’s players remained silent as their national anthem played before the game and didn’t celebrate their two goals in the 6-2 defeat.