Mostafa Ahmadi-Roshan, an academic who also worked at the Natanz uranium enrichment facility and another unidentified person were killed in the attack.
The blast happened after a motorcyclist stuck an apparent bomb to the car.
Both countries deny the accusations.
Iran’s Vice-President Mohammad Reza Rahimi told state television that the attack against Mostafa Ahmadi-Roshan would not stop “progress” in the country’s nuclear programme.
Mohammad Reza Rahimi called the killing “evidence of [foreign] government-sponsored terrorism”.
Local sources said Wednesday’s blast took place at a faculty of Iran’s Allameh Tabatai university.
Two others were reportedly also injured in the blast, which took place near Gol Nabi Street, in the north of the capital.
Mostafa Ahmadi-Roshan, 32, was a graduate of Sharif University and supervised a department at Natanz uranium enrichment facility in Isfahan province, semi-official news agency Fars reported.
“The bomb was a magnetic one and the same as the ones previously used for the assassination of the scientists, and the work of the Zionists [Israelis],” deputy Tehran governor Safarali Baratloo said.
Witnesses said they had seen two people on the motorbike fix the bomb to the car, reported to be a Peugeot 405. A second person died in the attack though the car itself remained virtually intact.
Reports at the time described Dr. Massoud Ali Mohammadi as a nuclear physicist, but it later appeared that he was an expert in another branch of physics.
There was also confusion as to whether the attack had any domestic political overtones because of reports about his apparent links to an opposition presidential candidate.
However, in August 2011, an Iranian man – Majid Jamali Fashi – was sentenced to death for the killing, with state authorities saying he was paid by Israel’s Mossad spy agency. Israel does not comment on such claims.
Of the latest attack, Fars reports that the bombing method appears similar to another 2010 bombing which injured former university professor Fereydun Abbasi-Davani, now the head of the country’s atomic energy organization.
There has been much controversy over Iran’s nuclear activities.
Tehran says its nuclear programme is for peaceful energy purposes, but the US and other Western nations suspect it of seeking to build nuclear weapons.
In a statement quoted on Iranian television on Wednesday, the country’s atomic energy agency said its nuclear path was “irreversible”, despite mounting international pressure.
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