The bill was drafted by a Republican and a Democrat and polls showed it was supported by around 90 per cent of the American public, but still fell six votes short of the 60 needed for passage.
"Instead of supporting this compromise, the gun lobby and its allies wilfully lied about the bill," Obama said, accusing Republicans of taking advantage of a "distortion" of Senate rules "to block it".
He warned that advocates of gun control would need to "sustain some passion" in order to defeat the power of the National Rifle Association (NRA).
"We can still bring about meaningful changes that reduce gun violence so long as the American people don't give up on it," he said "I see this as just round one."
Obama was joined by Gabrielle Giffords and introduced by Mark Barden, whose 6-year-old son Daniel was among the 20 children killed at the Connecticut primary school in December.
"What happened in Newtown can happen anywhere," Barden said through tears. "In an instant anydad in America could be in myshoes."
Only four Republicans, including Obama's 2008 election rival, John McCain, voted for the background checks bill, while four Democrats from gun-friendly states voted against it.
Several family members of victims of the Newtown massacre wept as Vice-President Joe Biden announced the bill's defeat. Patricia Maisch, a 64-year-old who helped tackle the gunman who fired a bullet into Giffords' brain during the 2011 Tuscon shooting, shouted, "Shame on you," as the result was read out.
The defeat is a political blow for the White House, which intensely lobbied members from both parties in the final days leading up to the vote and expended significant political capital making the case for stricter gun laws.
Biden was dispatched to Capitol Hill to rally support and Senator Frank Lautenberg, an ailing 89-year-old Democrat who has been absent from Congress for weeks with health problems, appeared on the floor in a wheelchair to cast his vote.
Senator Harry Reid, the Democrat Majority Leader, accused Republicans of putting "short-term political goals ahead of the American people" but vowed to try to revive the legislation at a later point.
Michael Bloomberg, the Mayor of New York and a national champion of gun control, called the vote "a damning indictment of the stranglehold that special interests have on Washington".
"More than 40 US senators would rather turn their backs on the 90 per cent of Americans who support comprehensive background checks than buck the increasingly extremist wing of the gun lobby," he said.
- Telegraph Group Ltd