Senate Majority Leader Harry Reid (D., Nev.) greeted Lautenberg with a handshake and kiss on the cheek.
"The Senate has spoken and there's no shortage of other important challenges to deal with, so it's time to move on," Toomey said afterwards in an interview. "If the question is, 'Do I regret what I have done?' I have no regrets. I wish that the outcome had been different."
In a speech on the Senate floor shortly before the vote, Toomey called his plan a "common sense" proposal that would not restrict lawful gun owners.
"This is a modest measure to increase the chances that we can keep guns out of the hands out people who have no legal right to have a gun," he said.
But opponents - including Republicans and Democrats from largely rural, conservative states - raised concerns that the plan would erode Second Amendment rights.
Toomey and Manchin stressed that their plan would only expand existing background checks, and that it included tough language banning creation of a "gun registry" - with 15 years in prison a potential punishment for officials violating that ban.
But opponents raised that fear over and over, pointing to gun control advocates' past calls for universal background checks.
"This is just the first assault on the Second Amendment. More background checks today, gun registration tomorrow. Who knows what will follow after this?" said Sen. Richard Shelby (R., Ala.).
Sen. Chuck Grassley (R., Iowa) added, "We should not start down the path to gun registration, as history shows where that leads."
"You can see the slippery slope of compromise of the second amendment that we're onto," he said.
Grassley and others said background checks would not have stopped the Newtown shooting, and he argued that criminals do not submit to background checks, so only law-abiding citizens are affected.
But his point seemed to be contradicted by another opponent, Sen. Lindsey Graham (R., S.C.), who said 80,000 gun purchases were stopped by failed background checks last year, including 9,000 involving would-be buyers with felony convictions.
Graham, though, said none of those people were prosecuted, so background checks should not be expanded. Instead, he argued that the current system should be bolstered before growing.
"Why create more paperwork where nobody's going to do something about it?" he said.
Toomey and Manchin - each gun owners who previously received "A" ratings from the National Rifle Association - fell short despite support from several other senators who have long backed gun rights.
Earlier Wednesday, Senate Majority Leader Harry Reid (D., Nev.) spoke out against "conspiracy theories" put forward by gun rights advocates, and called fears of a gun registry "shameful scare tactics."
"Maintaining law and order is more important than satisfying conspiracy theorists who believe in black helicopters and false flags," Reid said.
Sen. John McCain (R., Ariz.), one of the few Republicans voting "yes," gave an impassioned speech praising Manchin and Toomey.
"You may not win today, I say to my two colleagues, but I will say that you did the right thing," McCain said. "What they have tried to do today, I think, is an act that should be appreciated by those of us who many times avoid taking the tough decisions, and I think they're an example to all of us."
Pam Simon, shot in the chest in the 2011 shooting in Tuscon, Ariz., watched the vote from the gallery, along with many other shooting victims or loved ones of victims. Simon called the result, "terribly disappointing."
"We are going to come back," she said. "We are not going to forget this, obviously. More and more people are joining our club, sadly, and that's people who are survivors of gun violence."
A proposed ban on assault weapons also went down to defeat Thursday in the Senate. A ban on high-capacity ammunition magazines also failed.
The vote on Toomey and Manchin's amendment to a larger bill followed a day of last-minute lobbying and pleading by both sides.
"Many outside groups have mischaracterized the legislation. There have been many wildly inaccurate attributes suggested about this bill that are simply not true," Toomey said before the vote.
Gun-rights groups have raised fears that expanding background checks to cover gun shows and online sales would result in a "national registry" of firearm owners - even though the Toomey-Manchin bill explicitly bans creation of such a list.
Toomey said a leak of his talks with Manchin allowed rumors to begin before they could present the actual bill last week.
"I understand there are a lot of Pennsylvanians and a lot of Americans who have become, to varying degrees, distrustful of the federal government, and that I think is coloring people's," responses, he said.
Earlier in the day, Senate Minority Leader Mitch McConnell (R., Ky.) responded, "We should focus on keeping firearms out of the hands of criminals and those with mental issues that could cause them to be a threat to society.
"The government should not punish or harass law-abiding citizens in the exercise of their Second Amendment rights, and it's that focus on protecting communities and preserving our constituents' constitutional rights that will be my guide as we begin to vote on amendments to this bill."
Contact staff writer Jonathan Tamari at email@example.com or follow on Twitter @JonathanTamari. Read his blog 'Capitol Inq' at www.philly.com/CapitolInq.