Mr Fakhrizadeh, 62, was killed in an ambush near the capital of Tehran in a move guaranteed to raise tensions between Iran and the West further. Speaking on state television, Mr Rouhani said: “Our people are wiser than to fall in the trap of the Zionist regime Israel.
“Iran will surely respond to the martyrdom of our scientist at the proper time.”
Mr Fakhrizadeh is widely believed to be the mastermind of Iran’s bid to develop nuclear weapons.
His death could trigger a showdown between Iran and its enemies in the final weeks of Donald Trump’s presidency.
In addition, it is likely to complicate any effort by President-elect Joe Biden to reset US policy towards Iran in line with that of former President Barack Obama.
Neither the White House, Pentagon, US State Department nor the CIA has commented, and Mr Biden’s transition team is also staying quiet on the subject.
At least four scientists were killed between 2010 and 2012 in what Tehran claimed was a series of assassinations aimed at sabotaging its nuclear energy program.
Nevertheless, Iran continues to insist it has no ambitions to develop nuclear weapons.
The semi-official Tasnim news agency reported a car filled with explosives blew up close to Mr Fakhrizadeh’s vehicle at about 2.30pm local time yesterday.
Immediately afterwards, one of the assassins sprayed bullets into his car, reports claim.
One of Fakhrizadeh’s bodyguards was hit four times, and Fakhrizadeh himself was transported by helicopter to a hospital in Absard town at Damavand county 44 miles (70 km) east of Tehran, where he died.
Speaking to state television, one witness claimed there were repeated gunshots and Fakhrizadeh’s bodyguards clashed with the assassins.
Physicist Mr Fakhrizadeh was an officer in the Islamic Revolutionary Guard Corps and a professor at the Imam Hussein University in Tehran – as well as a top target for Mossad, according to the New York Times.
Israel Prime Minister Benjamin Netanyahu mentioned him by name in April 2018 during a presentation on Iran’s nuclear programme delivered days before Mr Trump pulled the US out of the 2015 JPOCA deal aimed at preventing Tehran developing nuclear weapons, citing repeated violations.
At the time, Mr Netanyahu said: “Remember that name, Fakhrizadeh.”