Four Eastern European countries were competing for three seats on the OPCW Executive Council, warring neighbours Russia and Ukraine, plus Poland and Lithuania.
Russia received the fewest votes, meaning it has no seat on the board for the first time in the organisation's history.
"OPCW is a very reputable international body and terrorists have no place in it," said Zelensky on X, formerly Twitter.
He said Russia's exclusion from the global body's council was a "logical result" of its aggression against his country.
"Its role in international affairs keeps diminishing and its isolation keeps growing," concluded Ukraine's president.
The Organisation for the Prohibition of Chemical Weapons won the Nobel Peace Prize in 2013 for its efforts to rid the world of the scourge of chemical weapons.
It played a key role during the Syria civil war when Damascus agreed to dismantle its chemical weapons arsenal and ship it for destruction under the aegis of the OPCW.
This deal stopped Barack Obama from launching military action after a chemical attack in the Ghouta suburb of Damascus that crossed the "red line" set by the then US president.
In July, the OPCW was able to announce the milestone that all the world's declared stockpiles of chemical weapons were "verified as irreversibly destroyed".
The United States had been the last of the signatories of the Chemical Weapons Convention, which came into effect in 1997, to destroy its stock.
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