Jones, who served as an adviser to the White House Council on Environmental Quality, had generated mounting criticism over the past week. He earlier issued back-to-back apologies -- first, for calling Republicans "assholes" during a videotaped address earlier in the year, and second for signing a petition in 2004 supporting the "9/11 truther" movement, which believes the Bush administration may have been involved in the Sept. 11, 2001, terror attacks.
The latter development, which came on top of several others, was perhaps the most devastating and led to calls for his resignation.
Jones stepped down late Saturday.
In a sharply worded statement, Jones said the controversy had become an unceasing distraction and assailed his critics.
"On the eve of historic fights for health care and clean energy, opponents of reform have mounted a vicious smear campaign against me. They are using lies and distortions to distract and divide," Jones said.
He said he had been "inundated" with calls from supporters urging him to "stay and fight."
"But I came here to fight for others, not for myself," he said. "I cannot in good conscience ask my colleagues to expend precious time and energy defending or explaining my past. We need all hands on deck, fighting for the future."
Nancy Sutley, chairwoman of the council Jones had been advising, said in a statement that she accepted the resignation, which was effective immediately, and called him a "strong voice for creating 21st century jobs that improve energy efficiency and utilize renewable resources."
The White House had stayed relatively quiet about Jones as the controversy developed, leading to speculation that he was on the way out. White House Press Secretary Robert Gibbs on Friday said only that he "continues to work in the administration."
Asked about the resignation on ABC's "This Week" Sunday, Gibbs would not say whether President Obama ultimately urged him to leave.
"The president and the CEQ accepted his resignation because Van Jones, as he says in his statement, understood that he was going to get in the way of the president and ultimately this country moving forward on something as important as creating jobs in a clean energy economy," Gibbs said, adding that Obama does not endorse Jones' statements and associations.
"He doesn't, but he thanks him for his service to the country," Gibbs said.
White House adviser David Axelrod said Obama did not order Jones out of the administration, but commended him for the decision to step down. Axelrod said Jones showed his "commitment" to his cause by removing himself "as an issue."
"The political environment is rough, so these things get magnified," he said on NBC's "Meet the Press."
Jones is considered a rising star in environmental circles. He wrote the New York Times bestseller "The Green Collar Economy" and has co-founded and worked with several groups dedicated to helping low-income and minority communities -- often through green jobs and better environmental policy. He got his start as a San Francisco-area activist.
But critics raised questions about his fitness for a White House-level office, pointing to his radical activities a decade ago as well as more recent controversial stances.
Sen. Kit Bond, R-Mo., had demanded that the Senate Green Jobs and New Economy Subcommittee conduct hearings to probe Jones' behavior and "reassure the American people that their government is safe from his divisive, incendiary and ultimately counterproductive sentiments."
Jones was a self-described "communist" during the 1990s and previously worked with a group dedicated to Marxist and Leninist philosophies. His comments, even in recent years, were often racially charged. He's blamed "white polluters and white environmentalists" for "steering poison" to minority communities. In 2005, he drew a distinction between white and black youths involved in shooting incidents by referencing the 1999 Columbine High School massacre.
"You've never seen a Columbine done by a black child. Never," Jones said. "They always say, 'We can't believe it happened here. We can't believe it's these suburban white kids.' It's only them!" he said. "Now, a black kid might shoot another black kid. He's not going to shoot up the whole school."
Such statements did not draw widespread attention until after a February video surfaced showing him calling Republicans "assholes" during an address in Berkeley, Calif. Jones apologized, but faced down his past again when it was discovered that he signed a 2004 statement calling on then-New York Attorney General Eliot Spitzer and others to launch an investigation into evidence that suggests "people within the current administration may indeed have deliberately allowed 9/11 to happen, perhaps as a pretext for war."
Jones afterward issued a blanket apology for his past statements and said the petition does not reflect his views. An aide said Jones didn't carefully review the petition at the time.
But that claim was swiftly disputed by 911Truth.org. "He did agree with that statement and he did sign on to it," 911Truth.org spokesman Mike Berger told FOX News in a telephone interview from St. Louis on Friday. Berger said the group's "original board members individually confirmed all signatories that had signed on to the statement."
The calls for resignation mounted. And lawmakers said the problems surrounding Jones spoke to the broader concern about so-called White House "czars," top advisers and officials who do not need congressional approval.
Rep. Mike Pence, R-Ind., became the first lawmaker to call on Jones to resign, issuing a press release calling for a moratorium on the hiring of additional "czars" until the vetting process in Jones' case could be properly investigated.
Sen. Lamar Alexander, R-Tenn., said these officials are an "affront to the Constitution."
"When you take all these people that make policy close to the president and the White House ... and aren't approved by the Congress, you're just adding fuel to the fire by those who think Washington is taking over everything," he told "FOX News Sunday."