After talks with Tajik President Imomali Rakhmonov, Putin said: "Our military presence in Tajikistan will not only guarantee our investment but will also guarantee stability in the region."
Criticised by nationalists for failing to defend its interests and presence in Central Asia, Russia has of late been keen to match the growth of US influence in the region.
With about 7000 soldiers, Moscow said the 201 Division's headquarters in Tajikistan would be Russia's largest military base on foreign soil.
At a joint news conference, Putin also announced deals to invest $2 billion in the former Soviet state.
Russian forces are said to have served as a stabilising factor in Tajikistan's 1992-97 civil war and a buffer against formerly Taliban-run Afghanistan.
However, Tajik officials have openly said they wanted the Russians out to let the government in the capital, Dushanbe, build on cooperation with the United States, as other neighbouring Central Asian leaders are doing.
Relations between the two improved drastically during the 2001 US-led military invasion of Afghanistan.
Tajikistan had been slow in implementing a 1999 pact granting the Russians a formal base, but promises of big investment and debt relief by Moscow changed that.
"Our military presence in Tajikistan will not only guarantee our investment but will also guarantee stability in the region"
Russian President Vladimir Putin
Last October, it opened a base in Central Asian Kyrgyzstan, where Nato established itself during the Afghan war.
Tajikistan also on Saturday formally confirmed Russia's ownership of a space control centre at Nurek, which was built in 1980 for the Soviet space programme.
Between the 201 Division and its border guards in Tajikistan, Russia has about 20,000 troops in the country.
Rakhmonov and Putin reiterated an earlier agreement to relocate the guards, who hold 90% of the Tajik-Afghan border, from Tajikistan by 2006.
The head of Russia's drugs control agency, Viktor Cherkesov, said Moscow would work hard to counter drug trafficking from Afghanistan.
"Our possibilities of discovering the channels of heroin trafficking from Afghanistan to the CIS (Commonwealth of Independent States), to Russia, have seriously increased," he said.