Grand Ayatollah Nasser Makarem Shirazi on Saturday condemned the death sentence as "cruel".
"Saudi Arabia should know that if it makes such a move, it will face hatred and anger of the entire Shia community and freedom-seeking Sunnis, and will also pay a heavy price," the ayatollah said in the shrine city of Qom.
The ayatollah also denounced the harsh conditions that Shias are facing in the Saudi kingdom.
"Unfortunately, Saudi Arabia’s Shias are under heavy pressure and are not free to perform their religious rites. Their rights are violated and they are deprived of many jobs," the grand ayatollah noted.
Ayatollah tasks Iranian Foreign Ministry to do utmost to help abolish death sentence on Sheikh Nimr
Also on Saturday, Ayatollah Lotfollah Safi Golpayegani urged the Iranian Foreign Ministry to help lift the death verdict on the Saudi cleric.
Ayatollah Golpayegani underscored that the death sentence against Sheikh Nimr has caused extreme regret among Shia Muslims and freedom-seekers.
He also urged Foreign Minister Mohammad Javad Zarif to make efforts in that respect.
The Society of the Followers of Imam Khomeini’s Line also issued a statement on Saturday condemning the verdict on Sheikh Nimr as "medieval".
Iranian universities and relevant student associations have also issued separate statements, denouncing the verdict against Sheikh Nimr. A number of university students and political activists also held a sit-in in front of Saudi the Arabian embassy in Tehran, protesting against the death sentence.
An Iranian MP has also given Saudi Arabia a warning that imposing death penalty on the religious figure will push the kingdom’s royal family closer to downfall.
"By making this move, Saudi Arabia will move closer to downfall, because the foundations of the Saudi regime are today more unstable than any other time," Mohammad Saleh Jokar, who sits on Parliament National Security and Foreign Policy Committee, told the Tasnim news agency on Saturday.
The lawmaker also lashed out at Riyadh for sponsoring the terrorists fighting in Iraq and Syria, saying it would undermine the interests of the Islamic world.
Read related coverage by Tehran’s Shahrvand daily
Appalling death sentence against Shia cleric must be quashed: Amnesty International
A death sentence passed against the dissident Shia cleric in Saudi Arabia after a deeply flawed trial is appalling and must be immediately quashed, said Amnesty International.
"The death sentence against Sheikh Nimr Baqir al-Nimr is part of a campaign by the authorities in Saudi Arabia to crush all dissent, including those defending the rights of the kingdom’s Shia Muslim community," Deputy Director of Amnesty International’s Middle East and North Africa Program Said Boumedouha said.
"The shocking death sentence against Sheikh al-Nimr followed by the arrest of his brother in court today illustrate the lengths Saudi Arabia will go to in their quest to stop Shia activists from defending their rights. Sheikh al-Nimr must be released and Saudi Arabia must end its systematic discrimination and harassment of the Shia community," Boumedouha added.
Amnesty said evidence for all the other charges he was convicted of came from religious sermons and interviews attributed to the cleric while Amnesty International’s review of these texts confirms that he was exercising his right to free expression and was not inciting violence.
"Some of the charges, such as disobeying the ruler, should not be offences as they criminalize the right to freedom of expression. Other charges are vague and have been used simply to punish him for his peaceful activities," he added.
"Sheikh al-Nimr’s trial has been seriously flawed. Eyewitnesses, whose testimonies were the only evidence used against him, were not brought to court to testify. This violates the country’s own laws. The Sheikh was denied the most basic means to prepare for his defense and was not represented by legal counsel for some of the proceedings because the authorities did not inform his lawyer of some dates of the hearings," Boumedouha stated.
The remarks came after Sheikh Nimr’s family reported on Wednesday that a Saudi judge has found him guilty of "sedition" and sentenced him to death.
Nimr, who is in his 50s, had been on trial since March 2013. He was found guilty of "disobeying" the kingdom’s rulers and taking up arms against security forces, his brother said.
Nimr’s family accused the court of ignoring the sheik’s "peaceful and non-violent approach," saying the case had caused "social and political discontent."
Nimr Baqr al-Nimr is an independent Shia Sheikh in al-Awamiyah, Eastern Province, Saudi Arabia. He is popular among youth and critical of the Saudi Arabian government. In 2009, he criticized the Saudi authorities and suggested secession of the Eastern Province if Saudi Shias’ rights were not better respected. During the 2011-2012 Saudi Arabian protests, al-Nimr called for protestors to resist police bullets using "the roar of the word" rather than violence, predicted the overthrow of the government if repression continued, and was seen by The Guardian as having "taken the lead in [the] uprising."
On 8 July 2012, al-Nimr was shot by police in the leg and arrested. Thousands of people protested in response in several protests in which two men were killed by police bullets. Al-Nimr started a hunger strike and appeared to have been tortured. The Asharq Center for Human Rights expressed concern for al-Nimr’s health during his hunger strike on 21 August, calling for international support to allow access by family, lawyer and human rights activists.
On 15 October 2014, al-Nimr was sentenced to death by the Specialized Criminal Court for "seeking ‘foreign meddling’ in Saudi Arabia, ‘disobeying’ its rulers and taking up arms against the security forces" and his brother, Mohammad al-Nimr, was arrested on the same day for tweeting information about the death sentence.