Terrorists murdered a great Iranian scientist, Zarif wrote in a tweet on Sunday, IRNA reported.
This cowardice, with serious signs of Israel's role, illustrates the warmongering of its desperate perpetrators, he added.
Iran calls on the world community, including the EU, to abandon the double standard and condemn this state terrorism, he noted.
Zarif has earlier released message in Russian, English, Arabic, German and Chinese languages reacting to the terrorist crime and has urging the international community to condemn state terrorism and hold responsible its perpetrators.
Fakhrizadeh, 59, was assassinated after being seriously wounded when assailants targeted his car and engaged in a gunfight with his bodyguards in Absard, a town just east of the capital Tehran.
The scientist, who headed the Defense Ministry’s Research and Innovation Organization, succumbed to injuries after medics failed to revive him.
The body of the assassinated scientist was taken to several revered Shia Muslim shrines ahead of his burial set for Monday.
Leader of the Islamic Revolution Ayatollah Seyyed Ali Khamenei on Saturday urged definitive punishment of those behind the Fakhriadeh assassination.
"Follow up on this crime and certainly punishing the perpetrators and those ordered it, and ... continue the scientific and technical efforts of this martyr in all of the fields he was working in,” Ayatollah Khamenei ordered the Iranian authorities.
Iran’s President Hassan Rouhani pointed at Israel, saying it acted as a US "mercenary" and killed Fakhrizadeh.
The New York Times said an American official and two other intelligence officials had confirmed Israel was behind the attack, without giving further details.
Fakhrizadeh’s name was mentioned multiple times in a presentation in 2018 by Israeli Prime Minister Benjamin Netanyahu, during which he repeated claims about the Iranian nuclear program.
Netanyahu described the scientist as the director of Iran’s nuclear program and said, “Remember that name, Fakhrizadeh.”
The regime has been behind the assassination of several Iranian nuclear scientists. It has also conduced cyberattacks on Iranian nuclear sites.