The pardons come with conditions and exceptions, state media reported.
According to the HRANA activist news agency, about 20,000 people have been arrested in connection with the protests, which the authorities accused Iran's foreign enemies of fomenting.
In a letter to Khamenei requesting the pardon, judiciary head Gholamhossein Mohseni Ejei said: "During recent events, a number of people, especially young people, committed wrong actions and crimes as a result of the indoctrination and propaganda of the enemy."Since the foreign enemies and anti-revolutionary currents' plans have been foiled, many of these youth now regret their actions," Ejei wrote.
The Norway-based Iran Human Rights group said this week that at least 100 detained protesters faced possible death sentences.
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