An embassy official said the plane had taken off with all the affected personnel and their families aboard.
Mr Obama ordered the expulsion in response to alleged hacking of the US Democratic Party and Clinton campaign during the 2016 presidential election.
President-elect Trump has promised a revelation about the allegations.
A spokesperson for the Russian embassy in the US, quoted by the TASS news agency, confirmed the departure of the plane from Washington on New Year's Day.
The aircraft was part of the Rossiya airline's special flight detachment group - the carrier for the president of Russia and other government officials.
Mr Obama's order had given the affected diplomats just 72 hours to leave the country.
Russian president Vladimir Putin had been expected to respond in kind, with the expulsion of US diplomats from its territory.
However, he later said he would not "stoop" to "irresponsible diplomacy", but rather attempt to repair relations once Donald Trump takes office.
Mr Trump praised the decision as "very smart".
He has previously said Americans "ought to get on with our lives" rather than sanction Russia.
But on New Year's Eve, he said he would reveal details "people don't know" about the incident in the coming days.
"I know a lot about hacking,'' he told reporters, "and hacking is a very hard thing to prove, so it could be somebody else."
He also said that he knows "things that other people don't know. And so they cannot be sure of the situation."
But he refused to provide details, saying he would make an announcement on "Tuesday or Wednesday".
The president-elect also suggested that computers could not be trusted with sensitive information, and recommended using pen and paper.
"You know, if you have something really important, write it out and have it delivered by courier, the old-fashioned way," he said.
"Because I'll tell you what - no computer is safe."
Thirty-five Russian diplomats expelled from the United States by President Barack Obama have left the country, Russian news agencies report.