In a statement, Supreme Leader Ayatollah Ali Khamenei called Mohsen Fakhrizadeh "the country's prominent and distinguished nuclear and defensive scientist."
Khamenei said Iran's first priority after the killing was the "definitive punishment of the perpetrators and those who ordered it." He did not elaborate.
Tel Aviv has yet to comment on a claim by President Hassan Rouhani that Israel was behind the killing on Friday of Mr Fakhrizadeh.
The slaying threatens to renew tensions between the U.S. and Iran in the waning days of Donald Trump's presidency, just as President-elect Joe Biden has suggested his administration could return to Tehran's nuclear deal with world powers from which Mr Trump earlier withdrew.
The Pentagon announced early on Saturday that it has sent the USS Nimitz aircraft carrier back into the Middle East.
Speaking to a meeting of his government's coronavirus task force, Mr Rouhani said Mr Fakhrizadeh's death would not stop its nuclear programme.
"We will respond to the assassination of Martyr Fakhrizadeh in a proper time," he said.
He added: "The Iranian nation is smarter than falling into the trap of the Zionists. They are thinking to create chaos."
Analysts have compared Mr Fakhrizadeh to being on a par with Robert Oppenheimer, the scientist who led the U.S.' Manhattan Project in World War II that created the atom bomb.
Friday's attack happened in Absard, a village just east of the capital that is a retreat for the Iranian elite. Iranian state television said an old truck with explosives hidden under a load of wood blew up near a car carrying Mr Fakhrizadeh.
As his sedan stopped, at least five gunmen emerged and raked the car with rapid fire, the semi-official Tasnim news agency said.
Hours after the attack, the Pentagon announced it had brought the USS Nimitz aircraft carrier back into the Middle East, an unusual move as the carrier already spent months in the region.
It cited the drawdown of U.S. forces in Afghanistan and Iraq as the reason for the decision, saying "it was prudent to have additional defensive capabilities in the region to meet any contingency."