Iran's players did not sing the national anthem during their World Cup opener against England in Qatar on Monday and Iranian television interrupted its broadcast.
Iranian activists believe the players' actions were a gesture of support for the anti-government protests in the country.
Many fans in the stadium were heard booing the anthem. Several Iranian supporters at the game expressed their solidarity with the protests.
Supporters wearing Iranian jerseys with the slogan "Women, Life, Freedom" could be seen at the Khalifa International Stadium.
One fan who did not want to be named said the Iranian authorities had killed women and children in the crackdown against the protests and that the demonstrations deserved support.
On Sunday, Iran captain Ehsan Hajsafi called for change and sent condolences to bereaved families.
Human rights activists estimate that more than 400 people have been killed so far in the nationwide protests in Iran.
