The deadline for the first government shutdown in 17 years was crossed because Republicans and Democrats could not agree on a "clean" continuing resolution to keep the government operating, CNN reported.
Office of Management and Budget Director Sylvia Burwell ordered federal agencies to execute their shutdown plans, Time magazine reported.
President Obama signed a bill to ensure the military continues to get paid during any shutdown, NBC News reported before the deadline.
"What the House Republicans are doing right now is voting for a government shutdown," House Budget Committee ranking member Chris Van Hollen, D-Md., said shortly before midnight.
"Instead of passing the bill already adopted by the Senate, which would guarantee that we keep the government open, they're rejecting that, and instead saying they want to go to conference, with 45 minutes left, which is a recipe for shutting down the government," Van Hollen said.
Obama earlier exhorted congressional leaders by phone to reach a budget deal rid of what the White House called "extraneous ideological riders."
Congress responded by playing ping pong with budget amendments that went nowhere.
With a shutdown looming, the president placed separate calls to Senate Majority Leader Harry Reid, Senate Minority Leader Mitch McConnell, House Speaker John Boehner and House Minority Leader Nancy Pelosi, the White House press secretary's office said in a statement.
"The president made clear to the Republican leadership that they must act, as the Senate has, to pass the bill that funds the government for six weeks that doesn't include any extraneous ideological riders," the White House statement said. "The president urged the House to bring up this clean continuing resolution for a vote tonight to keep the government open and avoid a shutdown."
In the calls, Obama "reinforced with the Republican leaders that he will continue to oppose any politically motivated attempts to defund or delay the Affordable Care Act, attempts which would never pass the Senate or become law," the statement said. "And he reiterated that he will not negotiate on the debt limit: Congress must pay the bills it has already incurred and avoid a devastating blow to our economy."
Obama "expressed his gratitude" to the Democratic leaders for standing with him.
After the Republican-controlled House volleyed once again with a spending resolution without funding for healthcare reform on a 228-201 vote, the Democrat-controlled Senate hit the budgetary ball back less than an hour later by voting 54-46 to table the GOP measure, Roll Call reported.
The House once again has attached ridiculous policy riders that are dead on arrival over here," Reid, D-Nev., said. "I've heard this story before, in fact just 6 hours ago."
Boehner said the vote to delay the healthcare reform was about "fairness," NBC News reported.
"I would say to the president: This is not about me," Boehner, R-Ohio, said. "This is not about Republicans here in Congress. It's about fairness for the American people."
NBC said several moderate Republicans expressed a desire to give up the hard-line stance on Obamacare.
"We've already launched two volleys unsuccessfully and now it's time to go on with the business of governing the country," Rep. Charlie Dent, R-Pa., told reporters. "The hourglass is already empty and it's time that we pass a clean CR [continuing resolution]."
The president warned earlier a government shutdown would hurt the American public and would not stop the new healthcare plan from taking effect.
"One faction of one party in one house of Congress in one branch of government doesn't get to shut down the entire government just to re-fight the results of an election," he said in a statement at the White House.
He said a shutdown would throw a wrench into the economy and threatens the progress people have made in recovering from the recent economic crisis.
"The idea of putting Americans' hard earned progress at risk is the height of irresponsibility," he said. "It does not have to happen."
Obama said he hopes in the 11th hour Congress -- and particularly the House -- "will do the right thing."
"Congress needs to keep our government open ... pay our bills on time and never, ever threaten the full faith and credit of the United States."
Obama said a shutdown would not stop the healthcare plan, which Republicans want to repeal, from taking effect on Tuesday.
"That funding is already in place," he said. "You can't shut it down."
The White House said a government shutdown could cost the economy $10 billion per week.
Obama's public exhortation to lawmakers came just hours after the Senate rejected an earlier House version that sought to gut funding for the Affordable Care Act in exchange for keeping the U.S. government running.
As promised by Democratic lawmakers in the Senate, the upper chamber voted 54-46 to reject that measure and strip language from it calling for a one-year delay of Obamacare and the repeal of the medical device tax.
"We are not going to be bullied," Reid, D-Nev., tweeted after the afternoon vote. "We've done everything we can to avoid a shutdown, and we've done it reasonably."
Obama said earlier he was not resigned to a shutdown.
"The bottom line is that the Senate has passed a bill that keeps the government open, does not have a lot of extraneous issues to it ... but that ensures that we're not shutting down the government and we're not shutting down the economy at a time when a lot of families out there are just getting some traction," Obama said during an earlier event with Israeli Prime Minister Binyamin Netanyahu.
"I've said before, Congress has two responsibilities: Pass a budget, pay the bills."
A shutdown would prompt federal agencies to stop a wide range of activities and furlough at least 825,000 of the government's more than 2 million workers, the White House said.
But essential services would continue, including the military and those related to national security, mail delivery, air traffic and law enforcement.
"If you're on Social Security, you will keep receiving your checks. If you're on Medicare, your doctor will still see you," Obama said.
Public support for a government shutdown fell from 53 percent two weeks ago to 45 percent as the midnight deadline loomed, Rasmussen Reports said Monday.