General Mohammad Ali Jafari said the Guards only intervened "in a limited way" against fewer than 15,000 "trouble-makers" nationwide, adding that a large number had been arrested.
Protests over economic problems broke out in Iran's second city Mashhad on December 28 and quickly spread across the country, turning against the regime as a whole.
A total of 21 people have died in the unrest, with protesters attacking government buildings and police stations in some areas.
"A large number of the trouble-makers at the centre of the sedition, who received training from counter- revolutionaries... have been arrested and there will be firm action against them," he said.
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Jafari spoke after thousands of pro-regime demonstrators took to the streets.
Chants of "Leader, we are ready" were heard as images showed thousands rallying in the cities of Qom, Ahvaz, Kermanshah and elsewhere.
The demonstrators waved Iranian flags and pictures of supreme leader Ayatollah Ali Khamenei, as well as placards saying "Death to seditionists".
General Jafari added those behind the protests had "intervened massively on social media" but that "once restrictions were started, the troubles reduced".
Telegram and Instagram were blocked on cellphones soon after the protests began on December 28.
Telecoms Minister Mohammad-Javad Azari Jahromi said Telegram would only be unblocked if it removed "terrorist" content.
"I had mail exchanges with the head of Telegram and I told him that the continuation of Telegram's activities is conditioned on the suppression of terrorist content," he said.
President Hassan Rouhani expressed hope in a phone call with Turkish counterpart Recep Tayyip Erdogan that the protests would end in a few days, a Turkish presidential source said.
The political establishment has closed ranks against the unrest, saying the protests were part of a foreign plot to destabilise the regime.
"The enemy is always looking for an opportunity and any crevice to infiltrate and strike the Iranian nation," Khamenei said yesterday.
US President Donald Trump said Iranians were trying to "take back" their government, extending a drumbeat of encouragement for the protests.
UN human rights chief Zeid Ra'ad Al Hussein called on the Iranian authorities to defuse tensions and investigate the deaths.
"It is incumbent on the authorities that their actions do not provoke a downward spiral of violence, as occurred in 2009," he said in reference to the last major protest movement against alleged election-rigging.
Even reformists in Iran, who backed the 2009 protests, have condemned the violence and the support the demonstrations have received from the United States.
But they also urged the authorities to address economic grievances.
Many have been turned off by the violence, which has contrasted with the largely peaceful marches in 2009.
But on the streets of the capital, there is widespread sympathy with the economic grievances driving the unrest, particularly an unemployment rate as high as 40 per cent for young people.