Iran is ruled by a Shia-led government.
Pictures posted on social media showed what appeared to be troops moving into Saudi areas where the Shia minority were due to protest.
However, Mr Nimr's brother called for a "peaceful" response to the execution, saying the family did not want to see further bloodshed.
The United States warned Saudi Arabia, which has a Sunni Muslim majority, that its execution of a prominent Shiite cleric behind anti-government protests "risks exacerbating sectarian tensions."
The Saudi embassy in Tehran has come under
attack from petrol bomb throwers amid a backlash against the execution
of a prominent Shia cleric.
Video footage posted on Twitter shows molotov cocktails
hitting the front of the mission and other pictures posted since appear
to show the building on fire.There was fierce criticism of Saudi Arabia after it executed 47 people at prisons around the country including Nimr al Nimr.
The Saudi army prepares to go into Qatif
The 56-year-old was a driving force behind the anti-government protests in the east of the Sunni-ruled country during the Arab Spring in 2011.
There have been outbreaks of unrest in neighbouring Bahrain, where demonstrators have already taken to the streets, and also in the eastern Iranian city of Mashhad, where the Saudi consulate was also overrun.
The list of those executed did not include Mr Nimr's nephew, Ali al Nimr, who was 17 when he was arrested in 2012.
Reports he had been sentenced to death sparked global outrage because of his age and the severity of the punishment.
Labour leader Jeremy Corbyn wrote to Prime Minister David Cameron urging him to intervene. The UK has close ties with Saudi Arabia.
Most on the list were detained after a series of attacks by al Qaeda between 2003 and 2006 in which hundreds of people were killed. Four, including Mr Nimr, were Shias accused of shooting policemen.
In a statement the Interior Ministry said the 47 had been convicted of adopting the radical "takfiri" ideology, joining "terrorist organisations" and implementing various "criminal plots".
All but two - an Egyptian and a Chadian - were Saudi nationals. The executions took place in 12 cities in Saudi Arabia, with four prisons using firing squads and the others beheading.
Saudi Arabia's top cleric, Grand Mufti Sheikh Abdulaziz al Sheikh, said taking their lives was a "mercy to the prisoners" as it would save them from committing more evil acts.
Criticism of Mr Nimr's execution has been led by Shia-dominated Iran, Saudi Arabia's main rival in the Middle East.
The Foreign Ministry warned the kingdom would "pay a high price", while a leading Iranian cleric, Ayatollah Ahmad Khatami, predicted the repercussions will "wipe" the Saudi ruling family "from the pages of history".
That view was shared by former Iraqi PM Nouri al Maliki who said in a statement Mr Nimr's death "will topple the Saudi regime".
The Lebanese militant group Hezbollah called it an "assassination" and the country's Supreme Islamic Shia Council described it as a "grave mistake".
In the UK, Shadow foreign secretary Hilary Benn said carrying out the death sentence on Mr Nimr was "profoundly wrong".
A demonstration was held outside the Saudi embassy in London in protest at the executions.
Shane Enright of Amnesty International UK said the death penalty was "unacceptable in all circumstances" and was particularly concerned that a number of "peaceful dissidents" had been killed, including Mr Nimr.
The international human rights group Reprieve said it showed the Saudi government was "continuing to target those who have called for domestic reform in the kingdom".
Mr Nimr's family said they were shocked but did not want his execution to result in any more bloodshed.
His brother Mohammed al Nimr told Reuters: "We hope that any reactions would be confined to a peaceful framework. No one should have any reaction outside this peaceful framework. Enough bloodshed."
Last year 157 people were put to death in Saudi Arabia, compared to 90 in 2014.
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