But leaders in Iraq and Iran have condemned the execution.
Former Iraqi prime minister Nuri al-Maliki said the decision to execute Nimr would topple the Saudi government "as the crime of executing the martyr (Mohammed Baqir) al-Sadr did to Saddam (Hussein)", referring to another prominent Shi'ite cleric killed by the Iraqi government in 1980.
Iranian cleric Ahmad Khatami called on the Muslim world to denounce the execution of al-Namir.
"I have no doubt that this pure blood will stain the collar of the House of Saud and wipe them from the pages of history", he was quoted as saying by the Mehr news agency.
Nimr's brother, Mohammed al-Nimr, was reported to have professed a hope that any protests held in the wake of the executions would be peaceful.
"Wrong misled and mistaken [are] those who think that the killing will keep us from our rightful demands", he wrote.
He added that Saudis take every action after consulting with the USA; however, they should know that Shia Muslims have no conflict with Sunnis but that they oppose Takfiris. He was sentenced to death in October 2014 and charged with crimes including disobeying the ruler, inciting sectarian strife and bearing arms against security forces.
"We have warned the concerned sides that any such reckless act means a catastrophe for the nation", said Sheikh Abdul-Amir Kabalan - deputy head of the influential Supreme Shiite Islamic Council, the main religious body for Lebanon's 1.2 million Shiites.
The wave of condemnation could harm Saudi Arabia's efforts to form an Islamic alliance against the jihadist militants of Islamic State.
45 of those executed were Saudi nationals one was from Egypt and another was from Chad, who were arrested from different locations at different times.
The 43 Sunni jihadists executed on Saturday, including several prominent al Qaeda leaders and ideologues, were convicted for attacks on Western compounds, government buildings and diplomatic missions that killed hundreds from 2003-06. The pace of Saudi executions has increased with the new king's rule.
Saudi Arabia and a mostly Gulf Arab alliance has been bombing the Houthis for nine months after the group, which hails from a Shi'ite sect based near Yemen's Saudi border, made an armed push in March against the embattled Yemeni government. And Iran's own clerics have already claimed that the beheading will cause the overthrow of the Saudi royal family.
But the list of those killed does not include Sheikh Nimr's nephew, Ali al-Nimr, who was 17 when he was arrested following the protests.
Human rights group Amnesty International had called the charges against Nimr vague and pronounced his death sentence "appalling".
"The execution of Nimr al-Nimr strengthens our existing concerns about the growing tensions and the deepening rifts in the region", it said.
Iran, which supports Shiite fighters in Yemen who are clashing with a Saudi-backed force there, strongly condemned the executions.
In 2009, Al-Qaeda announced a merger of its Saudi and Yemeni branches forming Al-Qaeda in the Arabian Peninsula (AQAP) - classified by the United States as the network's deadliest branch.
Some were beheaded with a sword while others were executed by firing squad, said interior ministry spokesman Mansur al-Turki.
The global human rights group Reprieve said it showed the Saudi government was "continuing to target those who have called for domestic reform in the kingdom".
