On a sun-splashed Friday afternoon in the Rose Garden, Obama praised Jones for keeping the country safe and “restoring American standing in the world.”
Obama described the job as one of the most difficult “in our government,” but said Jones had served admirably.
“You complete this assignment leaving your country safer and stronger,” Obama said to Jones.
Jones leaves the position as the administration winds down the war in Iraq but faces questions over the continuing mission in Afghanistan. The White House is also dealing with a war on terrorism that led to higher alerts in Europe this week.
Jones's resignation, effective in two weeks, comes as no surprise to either White House observers or national security staff. The general had been expected to leave the administration before the end of the year.
Jones had long been seen as somewhat of an outsider in Obama’s White House, while Donilon was seen as an insider who had Obama’s ear. Jones had reportedly expressed frustration with a lack of access to the president at times.
Donilon, however, has had rocky moments with the military brass in the past, according to Bob Woodward’s book “Obama’s Wars.” Defense Secretary Robert Gates is quoted in that book as saying it would be a “disaster” if Donilon succeeded Jones.
Gates praised Donilon on Friday, however, saying in a statement that he “has been in one of the toughest jobs in Washington and done it well.”
“I value the good working relationship I have with Tom and the rest of the Obama national security team and look forward to continuing our collaboration in tackling the many pressing security challenges facing our nation,” Gates said.
White House officials also pushed back on suggestions of a rift between Donilon and the Pentagon.
“We would certainly take issue with any sense that there's any kind of strain there,” a White House official said.
Donilon has a “fantastic relationship” with his counterpart on the Joint Chiefs of Staff Major Gen. James Cartwright, the official added. He said Donilon in advancing the president’s views “has asked for clarity and sharpness.”
In his own remarks at a Rose Garden ceremony, Jones said he admires the tireless Donilon, calling him “one of the hardest-working human beings I've ever seen.”
“You're the man who kept the trains running on time,” Jones said.
Obama credited Jones and his staff with helping to withdraw combat troops from Iraq, refocus the war on terror and in Afghanistan, restarting the Middle East peace process and resetting relations with Russia.
In naming Donilon to take over from Jones, the White House made the case that there will be a seamless transition for an administration that seen increased turnover in recent days and weeks.
According to one White House official, Donilon has already “interacted extensively almost as a principal already.”
White House Chief of Staff Rahm Emanuel departed one week ago to run for mayor of Chicago and was replaced by Pete Rouse, a senior adviser to the president.
Larry Summers, Obama’s chief economic adviser, is leaving after the election, and two other members of Obama’s team resigned over the summer.
Known for his work ethic and organizational abilities, Donilon has chaired more than 300 deputies’ committee meetings, and one official noted that there has “not been much leakage” from those.
Donilon has also been responsible for preparing Obama's daily intelligence briefing.
The White House said one Donilon's strengths is his relationships with members of Congress on both sides of the aisle and with Secretary of State Hillary ClintonHillary Rodham ClintonTrump must not pull a bait-and-switch on American workers Jewish groups divided over Hanukkah party at Trump hotel Colo. AG: Electoral College lawsuit could cause 'chaos' MORE.
Clinton praised Jones and Donilon in a statement, saying the administration would miss Jones but that Donilon was an able replacement.
"He has a proven ability to translate big-picture vision into concrete action," Clinton said. "Tom has been a trusted member of our team and has contributed to every major policy decision."
The announcement comes just a few months before Obama and his
national security team are set to gather to review the progress of the
administration's new strategy in Afghanistan.
Both Jones and Donilon were instrumental in Obama's decision to add 30,000 troops to the theater with a transfer of power beginning in July 2011.
This story was posted at 10:29 a.m. and updated 1:59 p.m.