The foreign ministry declared the pair persona non grata on the orders of Kosovo President Vjosa Osmani "because of harmful activities that risk endangering national security", she said on Friday.
Kosovo institutions are "determined to fight the malignant influence of the Russian Federation and its proxies in the region," she tweeted.
Russia's foreign ministry on Saturday called the move a "gross anti-Russian provocation" directed "against Russia and its constructive role in the Balkans".
In a statement it called on the UN mission in the former Serbian province to ensure "reliable security and the necessary conditions" for its personnel in Pristina.
Neither Osmani nor the foreign ministry disclosed the identities of the two diplomats.
There were no official details about their alleged activities which, according to Pristina, were not in line with their status.
Radio Television of Kosovo (RTK) on Saturday broadcast photos of the two diplomats leaving the premises of Russia's liaison office in Pristina and afterwards of their car crossing the border with Serbia.
It identified the two as Denis Vengerskii and Alexey Krivosheev and said their activities "incompatible with diplomatic status" were spotted by Kosovo's Intelligence Agency (AKI).
"It is not the first time Krivosheev has been declared 'persona non grata'," RTK said, adding that he had been expelled from Albania in January.
At the time, Albania's foreign ministry said Krivosheev was expelled over repeated failures to respect coronavirus infection control measures.
Russia strongly opposes ethnic-Albanian majority Kosovo's independence from Serbia which it declared in 2008.
Moscow became Belgrade's leading ally in lobbying against international recognition of Pristina.
However, Russia maintains its diplomatic presence in Pristina, basing it on the accreditation for a UN mission that for a decade governed Kosovo after the 1998-1999 war between ethnic Albanian guerrilla and Serbian forces.
