The State Security Service of Ukraine (SBU) said Kiev had declared Moscow's consulate general in Odessa "persona non grata" for conducting unnamed activities "incompatible" with his diplomatic work.
"The security service will continue to identify foreigners who work against our government using their diplomatic status as cover," the SBU said in a statement.
It added that the unnamed Russian diplomat had already left Ukraine.
International law does not require Kiev to explain its decision to ask a country's consular general to leave.
Most of the victims were Moscow backers who died when a government building in which they took cover caught fire after being pelted by Molotov cocktails launched by a Ukrainian nationalist mob.
The May 2014 incident came just a month into a war between Kiev forces and pro-Russian militias that has claimed the lives of 6,500 people in eastern Ukraine.
Kiev has since worked hard to restore calm in government-held Odessa -- home to Ukraine's largest port and a major tourist destination -- and no serious violence has been reported since.
Saakashvili has since launched a public campaign to eliminate corruption and cement Kiev's rule.
It was not immediately clear if the acting consulate general's ouster was in any way linked to the strongly pro-Western former Georgian president.
Yet Moscow's response was swift.
"This is another unfriendly step aimed at artificially fomenting tensions in our relations with Ukraine," Russia's Deputy Foreign Minister Grigory Karasin told the Interfax news agency.
