The president gave Emanuel a high-profile send-off in the East Room Friday. Obama called him "an incomparable leader of our staff, and one who we are going to miss very much."
The mood at the White House reflected that this was no ordinary staff change. Cabinet members and senior staff members packed the ornate East Room, for the official word that Emanuel was on his way out.
"We could not have accomplished what we've accomplished without Rahm's leadership," Obama said.
Emanuel is departing after nearly two grueling years to run for Chicago mayor.
Pete Rouse has been named interim chief of staff. He is a calm, trusted senior adviser to Obama who has spent much of his career as a chief of staff in the Senate.
"There is a saying around the White House: 'Let's let Pete fix it,"' Obama said.
The Associated Press contributed to this report.