"We have today withdrawn our support from Mrs Gloria Macapagal Arroyo, in order to end her unconstitutional and illegal occupation of the presidency," one of the leaders, Brig Gen Danilo Lim, wrote.
'Chaos and panic'
A five-hour overnight curfew has been imposed in Manila, starting at 2400 (1600GMT).
Interior minister Ronaldo Puno said it would allow the authorities to conduct "follow-up" security operations.
During the hotel assault, about 1,500 government troops had surrounded the building before an armoured personnel carrier smashed through the main entrance.
Tear gas and shots were fired, but there are no reports of casualties.
The BBC's Michael Barker at the scene said the lobby was covered with shattered glass and there were Christmas decorations on the floor.
A leader of the rebels, Sen Antonio Trillanes, said they were ending their action to save the lives of civilians and journalists inside the hotel.
He was arrested along with about two dozen soldiers.
Leonie Anning, a British tourist in Manila, told the BBC News website that she was in a nearby shop when she was evacuated and rushed onto the street.
"There was big chaos and panic," she said.
"There were many armed soldiers... and not knowing what's going on, it was pretty scary," she said.
However, Michael Whiting, the vice-chairman of the British Chamber of Commerce in Manila, told the BBC News website that his Filipino colleagues seemed "pretty apathetic".
"Most people have grown weary of attempts to overthrow the government," he said.
"World watching"
Robert Reyes, a priest who supported the rebels, said the violence was unnecessary.
"We did not really intend any violence - the violence came from the military," he said from the lobby before the rebels surrendered.
"You saw what happened - they had to ram a tank into the lobby of the hotel where there was not a single gunshot was fired. The whole world was watching - may the world have mercy on this government."
The Philippines has a history of insurrection and popular revolt.
Mrs Arroyo, whose popularity has been dented by long-standing corruption allegations, has already survived at least two coup plots and three attempts to impeach her during her time in office. Sen Trillanes, a navy lieutenant, was elected in May but has remained in military detention while on trial over a 2003 mutiny. Then renegade troops took over a shopping centre for a day, until they were overpowered by security forces.