A team of pathologists and cemetery officials hoisted the wooden caskets of Ceausescu and his wife, taking samples from the corpses, before reburying the coffins.
Some Romanians doubt that the Ceausescus, who were executed in 1989 after fleeing mass protests in Bucharest, were really buried in the cemetery.
The couple's three children, of whom just one son, Valentin, is still alive, have repeatedly said they doubted their parents had actually been buried there.
Wednesday's exhumation is the latest development in a five-year court case that has seen Ceausescu's children battling to identify the bodies.
Oprean's wife, Zoia Ceausescu, had sued the defence ministry in 2005, saying she was not sure that her parents were buried in the cemetery.
She died of cancer in 2006 and her brother Valentin took up the case.
Cornel Muntean, a cemetery worker, told The Associated Press news agency that Ceausescu was dressed in a thick grey overcoat.
Oprean said he planned a full funeral ceremony if the tests, which will take several months, confirmed the remains were those of his inlaws.
Nicolae Ceausescu ruled Romania from 1965 until 1989, when communist governments fell across central and eastern Europe.
He was toppled after Romanians led protests against the communist government, angered and exhausted by years of rationing as the leader tried to pay off the country's foreign debt.
Ceausescu had stifled dissent with his Securitate secret police, which were believed to have 700,000 informers in the nation of 22 million.
Following their summary trial and execution on Christmas Day, authorities decided to bury the Ceausescus at night under crosses bearing false names to avoid the tombs being desecrated, witnesses said.
Dozens of people nostalgic for the communist era gathered around the graves following the exhumation.
"Our life was better then, we had everything we needed," one woman told reporters.
Twenty years after the toppling of the communist government, many of the dramatic events of the time are still shrouded in mystery.
Some Romanians still question the circumstances of the Ceausescus' execution, the aftermath of which was broadcast around the world.