The Organisation for the Prohibition of Chemical Weapons (OPCW) said in a statement that the biomarkers in his blood and urine had "similar structural characteristics as the toxic chemicals belonging" to the Novichok group.
The findings confirm results released by Germany, where Navalny was treated after falling ill on a flight in Siberia on Aug. 20. Berlin asked the OPCW to take samples from Navalny and test them after German doctors concluded he had been poisoned with Novichok.
The German government said on Tuesday it would discuss with partners what action to take after findings from the global chemicals watchdog confirmed that Kremlin critic Alexei Navalny was poisoned with a nerve agent in the Novichok family.
Navalny was airlifted to Berlin for treatment after falling ill on a flight in Siberia on Aug. 20 and Germany and other Western governments have called on Russia to help in investigations into what happened.
Navalny has been discharged from hospital and plans to return to Russia. Moscow has denied accusations by Navalny that it was involved in the poisoning.
"The next steps will be discussed in the Executive Council of the Organisation for the Prohibition of Chemical Weapons (OPCW) and with the EU partners," German government spokesman Steffen Seibert said in a statement.
"Any use of chemical weapons is a serious matter and cannot remain without consequences," he added.
Options include targeted asset freezes or travel bans on Russian individuals deemed to be involved in the Navalny case, economic sanctions and halting the Nord Stream 2 pipeline that is being built to carry gas directly from Russia to Germany.
"This again confirms the unequivocal proof that Alexei Navalny was the victim of an attack with a chemical nerve agent of the Novichok group," said Seibert in the statement.
Western governments have called for sanctions against Moscow over the case. Russia denies any involvement and has said it doubts Navalny was poisoned.
"No doubt Novichok nerve agent used to poison Alexey #Navalny," Britain's delegation at the OPCW said on Twitter. "Any use of a banned chemical weapon is a matter of great concern."
Novichok, a Soviet-era nerve toxin, was also used to poison a former Russian spy in England in 2018. The OPCW's member states agreed last year to ban chemicals in the Novichok family, a ban that went into effect four months ago.