A statement on the Kremlin's website posted Monday afternoon said Antonov was appointed by presidential decree.
Kislyak has been a central figure in the U.S. Russian Federation investigations - because he met with several of President Donald Trump's representatives before, during and after the November presidential election.
Kislyak has been at the eye of the storm over his meetings with senior campaign aides to Donald Trump during the presidential race.
The move comes as the US embassy in Moscow announced it is suspending all non-immigrant visa processing for Russians until September 1 in response to the staff cuts ordered by the Kremlin, The Sun reports.
He was appointed the deputy foreign minister in charge of military and political security in December 2016 after serving as the country's deputy defence minister for six years.