It added that Fakhrizadeh, who headed the defence ministry's reasearch and innovation organisation, was later "martyred" after medics failed to revive him.
Fakhrizadeh, once described by Israeli Prime Minister Benjamin Netanyahu as the father of Iran's nuclear weapons programme, had been travelling in a car near Absard city in Tehran province's eastern Damavand county.
Iran's Foreign Minister Mohammad Javad Zarif said there were "serious indications of an Israeli role" in the scientist's assassination.
"Terrorists murdered an eminent Iranian scientist today," Zarif wrote on Twitter.
"This cowardice -- with serious indications of Israeli role -- shows desperate warmongering of perpetrators," he added.
He also called on the international community to "end their shameful double standards & condemn this act of state terror."
Fakhrizadeh's assassination comes less than two months before Joe Biden is to take office as US president.
Biden has has promised a return to diplomacy with Iran after four hawkish years under incumbent US President Donald Trump, who withdrew from the Iran nuclear deal in 2018 and began reimposing crippling sanctions.
Trump said at the time that the deal known formally as the Joint Comprehensive Plan of Action (JCPOA) it did not offer sufficient guarantees to stop Tehran from acquiring an atomic bomb. Iran has always denied it wants such a weapon.
This story has been published from a wire agency feed without modifications to the text. Only the headline has been changed.