State TV swiftly blamed Israel for the attacks.
At least two other Iranian nuclear scientists have been killed in recent years in what Iran has said is part of a covert attempt by the West to damage its controversial nuclear programme.
Iran insists that its interest in developing a nuclear industry is to generate power but the technology could also be used for weapons.
Head of the country's nuclear operation Ali Akbar Salehi, issued a stern warning as he rushed to hospital to see the surviving scientist, Fereidoun Abbasi.
"Don't play with fire. The patience of the Iranian nation has limits. If it runs out of patience, bad consequences will await enemies," he said.
Mr Salehi, one of Iran's vice presidents, was apparently referring to Israel and the US, which Iran alleges are trying to damage its nuclear programme.
Tehran's uranium enrichment program is at the centre of a bitter row between Iran on one side and the US and its allies on the other. Uranium enrichment is a process that can be used to produce both nuclear energy and nuclear weapons.
Some countries suspect Iran is trying to make nuclear weapons, an allegation the government denies. Tehran's refusal to halt uranium enrichment has brought on multiple rounds of UN sanctions against the country.
Several active armed groups oppose Iran's ruling clerics, but it is unclear whether they could have carried out the apparently co-ordinated bombings in the capital. Most anti-government violence in recent years has been isolated to Iran's provinces such the border with Pakistan where Sunni rebels are active and the western mountains near Iraq where Kurdish separatists operate.
The attackers, who escaped, drove by their targets on motorcycles and attached the bombs as the cars were moving. They exploded shortly afterwards.
The attacks bore close similarities to another in January that killed Tehran University professor Masoud Ali Mohammadi, a senior physics professor. He died when a booby-trapped motorcycle exploded near his car as he was about to leave for work.
In 2007, state TV reported that nuclear scientist Ardeshir Hosseinpour died from gas poisoning. A one-week delay in the reporting of his death prompted speculation that Israel's Mossad spy agency was to blame.
Iran has continued to portray its nuclear programme as being under constant pressure from the West and its allies. These include alleged abductions of nuclear officials and, more recently, a computer worm known as Stuxnet that experts say was calibrated to destroy uranium-enrichment centrifuges by sending them spinning out of control.