"Two separate meetings took place - one with President Bashar al-Assad and one with Vice-President Faruq al-Shara," the spokeswoman said on Tuesday.
"Commissioner Brammertz went to Damascus today to hold the meetings referred to in the independent international investigation commission's" report of March 14, she said.
The spokeswoman, who asked not to be named, did not disclose more details on the meetings or whether Brammertz had returned to Lebanon where the UN probe commission is based.
Two UN reports have implicated senior Syrian officials in al-Hariri's murder in a massive bomb blast on the Beirut seafront that also killed another 22 people on February 14, 2005.
The UN reports also criticised the Syrian government for failing to cooperate more with the international investigation.
It was the first time that the UN investigators met al-Assad who confirmed last month that he had agreed to receive them, while insisting it would be a "meeting and not an interrogation" over al-Hariri's murder.
Syria, which had been the main powerbroker in Lebanon for some three decades before it pulled out its troops following al-Hariri's murder, has strongly denied any involvement in al-Hariri's murder and accused the United Nations of bias.