Kim Jong Yang will become the new head of the global crime fighting organisation.
Current vice president Major General Alexander Prokopchuk had been in the running for the top job after the incumbent, China’s Meng Hongwei went missing in September.
But the possibility of having a Russian heading the organisation had drawn protests from the UK and US.
There were concerns about Russia’s previous applications for Interpol “Red Notices” (international arrest warrants) to target Kremlin critics.
Tom Tugendhat and Yvette Cooper, chairs of the influential Commons foreign and home affairs select committees, had said that having Mr Prokopchuk being elected would be “the latest nail in Interpol’s coffin”.
They said his role in the Kremlin, heading the department that deals with Interpol requests, had seen numerous “politically motivated” decisions.
US National Security Council spokesman Garrett Marquis had said that “the Russian government abuses Interpol’s processes to harass its political opponents”.
In an open letter this week, a bipartisan group of US senators had said choosing Mr Prokopchuk would be like “putting a fox in charge of a henhouse”.
But Russian presidential spokesman Dmitry Peskov described the letter as a “vivid example” of attempts to interfere with the vote and Moscow’s interior ministry said it was a “foreign media campaign aimed at discrediting Russia’s candidate”.
Responding to the result of the vote, the Kremlin said it regretted that its candidate was not chosen, adding that it was “Obvious there was outside pressure on the vote”, according to Interfax news agency.
Both the US and UK had instead stated their preference for Mr Kim, who has been acting president since Mr Meng’s disappearance.
Mr Kim secured at least two-thirds of the votes cast by Interpol’s 192 member countries at the organisation’s general assembly in Dubai on Wednesday.
He will serve until 2020.
His main role is to chair the organisation’s General Assembly, while day-to-day operations are handled by the secretary general Juergen Stock.