Russia's Sergei Lavrov and Latvia's Maris Riekstins also signed a cooperation deal on social security, and agreements on the status of soldiers' burial sites in both countries.
The border treaty, drafted back in 1997, aims to put an end to a long-running territorial dispute between the two former Soviet republics.
It was ratified by the countries' parliaments and presidents earlier this year, and Latvia's Constitutional Court gave its final seal of approval in late November.
In line with the treaty, a 9.5-kilometer (6-mile) sector of the border is to be moved 30 meters (98 feet) to the west, making the strip Russian territory.
By signing the treaty, European Union member Latvia has officially recognized its post-Soviet borders with Russia, dropping its earlier territorial claims to the Pytalovsky District in Russia's Pskov Region, part of the Baltic country until World War II.
Speaking at a news conference after exchanging the ratification documents, Lavrov urged the Latvian government to step up efforts to settle the issue of non-residents in Latvia.
"We understand that the problem of ethnic minorities in Latvia is a complicated one, and cannot be solved in an instant; but taking into account the current tempo of naturalization, the problem of non-residents could drag on for decades," the Russian diplomat said, calling such a scenario "unacceptable."
The minister said that Russia would also like to simplify the visa regime for traveling between the states.
"Work on this has begun, but it is far from concluded," he said.
Lavrov said that although work in this direction has been started, it is still far from completion. He also expressed his hope that the State Duma would approve a draft law on granting more powers to Russian ambassadors in issuing entry visas for ethnic Russians.
