Saudi Arabia’s execution of a prominent Shiite cleric and 46 other men has prompted outrage in parts of the Middle East, including the kingdom’s embassy in Tehran which was stormed by protesters and set on fire.

The men, mostly suspected Al Qaeda members but also Sheikh Nimr al-Nimr, were executed after being convicted of adopting the radical “takfiri” ideology, joining “terrorist organisations” and implementing various “criminal plots”.

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“The divine hand of revenge will take the Saudi politicians by the throat,” Iran’s Supreme Leader Ayatollah Ali Khamenei warned the government on Sunday.

A crowd of angry protesters hurled petrol bombs and stormed the Saudi Arabian embassy in Tehran early on Sunday morning (local time) before being cleared out by police.

Pictures and video on social media showed parts of the building’s interior on fire and smashed furniture inside one office.

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Journalist Sobhan Hassanvand, from the local Shargh newspaper, filmed protesters throwing what appeared to be Molotov cocktails and trashing the embassy.

The Iranian Students News Agency (ISNA) said the embassy caught fire and the interior was destroyed.

“The police are everywhere and have dispersed the demonstrators, some of whom have been arrested,” ISNA said

Bahraini women protest in the village of Jidhafs against the execution of Nimr al-Nimr. AFP: Mohammed Al-Shaikh

Another witness who lives locally said he saw members of the Basij militia position themselves in front of the embassy building.

“They were throwing Molotov cocktails at the Saudi embassy,” the witness said.

“It began with 15 or 20 people but I saw others joining them from nearby streets.”

Iran’s Foreign Ministry issued a statement calling for calm and urging protesters to respect the diplomatic premises, the Entekhab news website reported.

Iraqi leaders question Saudi alliance

Iran’s hardline Revolutionary Guards promised “harsh revenge” against the Saudi Sunni royal dynasty for the execution of Sheikh Nimr, considered a terrorist by Riyadh but hailed in Iran as a champion of the rights of Saudi Arabia’s marginalised Shiite minority.

Sheikh Nimr, the most vocal critic of the dynasty among the Shiite minority, had come to be seen as a leader of the sect’s younger activists, who had tired of the failure of older, more measured leaders to achieve equality with Sunnis.

In Iraq, whose Shiite-led government is close to Iran, prominent religious and political figures demanded that ties with Riyadh be severed, calling into question Saudi attempts to forge a regional alliance against Islamic State, which controls swathes of Iraq and Syria.

The head of the Shiite Dawa party’s parliamentary bloc, Khalaf Abdelsamad, urged Baghdad to close the Saudi embassy, expel the ambassador and “execute all Saudi terrorists in Iraqi prisons”.

Iraqi Prime Minister Haider al-Abadi, a member of the Dawa party, expressed “great shock” and warned of the destabilising potential of the execution.

“Freedom of speech and peaceful opposition are basic human rights granted by divine and international laws. Violating them impacts the region’s security, stability and social fabric,” he said in a statement.

In the holy Shiite city of Karbala, south-west of Baghdad, hundreds demonstrated and urged the closure of the newly opened Saudi embassy.

A Shiite protester carries a poster of Sheikh Nimr al-Nimr. Reuters: Khaled Abdullah

“We will reap your souls, Saud and Khalifah,” one of the banners read, referring to the Saudi and Bahraini ruling families.

“I swear to God that the sheikh’s blood was not spilled in vain,” one of the protesters said.

“We will make the Earth shake under your feet,” he added, addressing Saudi’s royal family.

Demonstrations also continued in Saudi Arabia, where hundreds of protesters marched through Qatif district in chanting “Down with the Al Saud!”, the name of the ruling Saudi royal family.

In Lebanon, the powerful Shiite movement Hezbollah accused Riyadh of “assassinating” Sheikh Nimr.

Syrian Information Minister Omran Zohbi described the executions as a crime, saying they were “an assassination of freedoms and human rights”.

He urged international organisations to hold Riyadh accountable, saying “this group assassination is a horrific humanitarian and political crime”.