The Il-96 jet brought home 46 Russian diplomats and their family members, the state TASS news agency said.
Russian television showed passengers disembarking from the plane while several buses waited to pick them up.
A second plane was expected to arrive in the Russian capital later Sunday.
In total, 171 people -- diplomats and their families -- were scheduled to leave the US.
Washington joined a score of Britain's allies in expelling Russian diplomats in response to a nerve agent attack against a former double agent, with more than 150 ordered out of the US, EU members, NATO countries and other nations.
The US announced it would send home 60 diplomats -- which it alleges are "spies" -- posted around the country and at the Russian mission to the United Nations, as well as closing Russia's consulate in Seattle.
Moscow responded by expelling 60 US diplomats and closing Washington's consulate in Saint Petersburg.
The tit-for-tat measures came in retaliation to the coordinated expulsion of Russian diplomats by Britain and its allies over the nerve agent attack against former double agent Sergei Skripal and his daughter Yulia in the English city of Salisbury on March 4.
It is the biggest wave of diplomatic expulsions between Russia and the West in recent memory.
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