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.
Several Iranian nuclear scientists have been assassinated in recent years, with Iran blaming Israel and the US.
Both countries deny the accusations.
Iran's Vice-President Mohammad Reza Rahimi told state television that the attack against Mr Ahmadi-Roshan would not stop "progress" in the country's nuclear programme.
He 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.