Moscow and London have each expelled multiple embassy staff over the last decade, trading accusations of espionage.
Expulsions from one side have typically been followed by a tit-for-tat response from the other.
The diplomat, named as 29-year-old embassy secretary Albertus Gerhardus Janse Van Rensburg, was expelled for engaging in "subversive intelligence activities that threaten Russia's security", Russia's FSB security service said.
"A decision was made to strip Janse Van Rensburg of his accreditation, and he was ordered to leave Russia within two weeks," it added.
The Russian foreign ministry said it had summoned Britain's charge d'affaires over the incident and warned the United Kingdom not to retaliate.
Britain accused Russia of waging an "aggressive and coordinated campaign of harassment".
"The accusations made today by Russia against our diplomats are complete nonsense," a foreign ministry spokesperson said, adding Russia was "pumping out malicious and completely baseless accusations about their work".
Relations between London and Moscow, currently at a low point over the Ukraine war, have been strained by spying allegations for decades.
In 2006, former FSB officer and Russian defector Alexander Litvinenko was killed in London, poisoned by polonium in what British investigators said was a hit by the Russian secret service.
In 2018, the UK said Russian double agent Sergei Skripal was poisoned with a Novichok nerve agent in the British cathedral city of Salisbury.
One member of the public was killed after handling the delivery device, a discarded perfume bottle, triggering the largest Western expulsion in decades of Russian diplomats alleged to be spies.