"I believe that this signature will open a new page for co-operation between our two countries," he said.
"This is a win-win situation, no one stands to lose from this agreement ... the entire world community has won."
Obama thanked his Russian counterpart for his "extraordinary leadership", but stressed that the pact was just one step towards further cuts in the two countries' nuclear arsenals.
"Today is an important milestone for nuclear security and non-proliferation, and for US-Russia relations," he said.
Laurence Lee, Al Jazeera's correspondent in Prague, said the treaty still has to be ratified by the US Congress and the Russian Duma.
"The Russians are also still saying that if they don't like the shape of Barack Obama's new missile defence shield, which replaces George Bush's proposal, then they still reserve the right to pull out of this," he said.
"Even the Americans accept that it can only be seen as a precursor to a wider conversation with the rest of the world about Barack Obama's vision of a nuclear-free world."
Medvedev said he still hoped a compromise could be reached between Moscow and Washington on the shield plans, which would see land and sea-based missile systems deployed to defend against what the US says is a growing Iranian threat.
The Kremlin added that the nuclear agreement was only "capable of life" if Washington was restrained in its missile programme.
"The treaty ... can only function and be capable of life in conditions where there is no qualitative and quantitative expansion of a possible US missile defence system," it said in a statement.
'Not so substantive'
Thursday's agreement aims to reduce the number of deployed warheads by 30 per cent from the levels set in the last major US-Russian disarmament treaty in 2002, specifying limits of 1,550 nuclear warheads for each of the two countries.
Richard Weitz, the director of the Hudson Institute's Center for Political-Military Analysis, told Al Jazeera the treaty, in terms of nuclear cuts, is not so substantive.
"In terms of the reductions themselves, the treaty is not so substantive, it is, however, a modest confidence boosting measure.
"The limits are somewhat lower than in previous treaties. But if we hadn't reached this treaty people would become very concerned," he said.
Medvedev arrived in Prague from Bratislava, the capital of neighbouring Slovakia, where he commemorated the 65th anniversary of the city's World War II liberation.
He will leave for Moscow after a joint ceremonial lunch on Thursday afternoon.
Obama will meet 11 European leaders on Thursday evening, spend the night in Prague and leave around noon (10:00 GMT) on Friday after bilateral talks with Czech leaders.