The resignation was disclosed without advance notice by the White House in a dead-of-the-night e-mail on a holiday weekend. It came as Obama is working to regain his footing in the contentious health care debate.
Jones, who specialized in environmentally friendly "green jobs" with the White House Council on Environmental Quality, was linked to efforts suggesting a government role in the Sept. 11 attacks and to derogatory comments about Republicans.
Gibbs said /*Obama*/ did not endorse Van Jones' comments but thanked him for his service.
"What Van Jones decided was that the agenda of this president was bigger than any one individual," Gibbs said on ABC's "This Week.
Recent news reports cited a derogatory comment Jones made in the past about Republicans, and separately, of Jones' name appearing on a petition connected to the events surrounding the Sept. 11 attacks. That 2004 petition had asked for congressional hearings and other investigations into whether high-level government officials had allowed the attacks to occur.
"On the eve of historic fights for health care and clean energy, opponents of reform have mounted a vicious smear campaign against me," Jones said in his resignation statement. "They are using lies and distortions to distract and divide."
Obama's top political adviser, David Axelrod, said on NBC's "Meet the Press" that Jones "showed his commitment to the cause of creating green jobs in this country by removing himself as an issue."
Howard Dean, former head of the Democratic National Committee, told "Fox News Sunday" that he thought Jones "was brought down and I think it's too bad. Washington's a tough place that way, and I think it's a loss for the country."
Dean, a former Vermont government and Democratic presidential candidate, added: "All of us campaigning for office have had people throw clipboards in front of our face and ask us to sign. And he learned the hard way you ought not to do that. But I don't think he really thinks the government had anything to do with causing 9/11."
Jones said he has been "inundated with calls from across the political spectrum urging me to stay and fight." But he said he could not in good conscience ask his colleagues to spend time and energy defending or explaining his past.
Jones said in an earlier statement that he did not agree with the petition's stand on the Sept. 11 attacks and that "it certainly does not reflect my views, now or ever."
As for his other comments he made before joining Obama's team, Jones said, "If I have offended anyone with statements I made in the past, I apologize."
Despite his apologies, Republicans demanded Jones quit. Rep. Mike Pence of Indiana said in a statement, "His extremist views and coarse rhetoric have no place in this administration or the public debate." Missouri Sen. Christopher "Kit" Bond said Congress should investigate Jones's fitness for the job.
Fox News Channel host Glenn Beck repeatedly denounced Jones after a group the adviser co-founded, ColorofChange.org, led an advertising boycott against Beck's show to protest his claim that Obama is a racist.
The president of Beck's media organization, Christopher J. Balfe, said the commentator had begun focusing on Jones' "radical beliefs" on July 16, before the group started taking on Beck.
But James Rucker, the organization's executive director, has said Jones had nothing to do with ColorofChange.org now and didn't even know about the campaign before it started.
Jones, well-known in the environmental movement, was a civil-rights activist in California before shifting his attention to environmental and energy issues. He is known for laying out a broad vision of a green economy. Conservatives have harshly criticized him for having left-wing political views.
Nancy Sutley, who heads the White House environmental council, said Jones "had been a strong voice for creating jobs that improve energy efficiency and utilize renewable resources.'
Associated Press writer Philip Elliott contributed to this report.
On the Net:
Council on Environmental Quality: http://www.whitehouse.gov/administration/eop/ceq/
Glenn Beck show: http://www.glennbeck.com