Moldova, a WTO member since July 2001, agreed to sign the protocol following Russian President Vladimir Putin's promise to reverse an embargo on Moldovan wine, the country's main export.
Moscow introduced the ban in March, citing food safety concerns, but Moldova, which had until then been selling 80% of its wine exports in Russia, said the move was politically motivated.
The two post-Soviet countries have long been at loggerheads over Transdnestr, Moldova's predominantly Russian province that broke away from central government control after a bloody war in the 1990s.
Earlier this year, Russia imposed a ban on wine and mineral water imports from Georgia, another WTO member with which Russia is yet to complete bilateral talks on its accession to the world's largest trade body.
Georgia's foreign minister, Gela Bezhuashvili, said Tuesday his country was willing to continue WTO accession talks with Russia, but that it would not sign a final protocol until after Moscow lifted its economic blockade and legalized its checkpoints on the border with the breakaway Georgian regions of Abkhazia and South Ossetia.
Russia's already strained relations with its smaller southern neighbor worsened further following the brief detention of four Russian army officers on espionage charges in September. Moscow responded to the move by cutting transportation and postal links with the ex-Soviet Caucasus nation and deporting hundreds of Georgian migrants.
Russia will also have to sign protocols on the completion of bilateral talks over its WTO accession with Salvador, Guatemala and Costa Rica.
The Russian economics ministry expects to complete multilateral talks on the country's accession to the WTO by the middle of 2007.