The end to their short-lived mutiny followed prolonged talks with government officials even as two deadlines served on them by President Gloria Arroyo to surrender lapsed.
"The crisis in Makati is over," a smiling Arroyo announced on nationwide television.
"This has been a triumph for democracy," an immensely relieved president added.
The heavily-armed mutineers were seen shortly afterwards defusing the explosives they had laid around the commercial complex.
They capitulated after holding out for most of the day.
President Arroyo had earlier set them a deadline of 1700 (0900 GMT), later extended by another two hours, to either surrender or face an assault.
But early signs of the mutineers caving in came when 50 or so of them walked out of the complex and surrendered themselves some hours ahead of the first deadline.
In wearing down the mutineers, Arroyo struck a tough posture and assumed special powers by declaring a state of rebellion.
“ Past this deadline, the Chief of Staff is authorised to use reasonable force to dislodge your group quickly and efficiently and arrest you,” Arroyo had earlier said.
A group of 200 mutineers took over the upmarket Ayala Centre in the capital’s Makati district early on Sunday, demanding the resignations of the President and her cabinet.
Surrounded by pro-government troops, the rebels sported red armbands and rigged the areas with explosives. Dressed in army camouflage, they accused Arroyo’s government of breeding corruption and sponsoring terrorism.
The mutineers, comprising junior officers and enlisted men, earlier allowed up to 300 foreigners and residents trapped in the commercial complex to leave on a fleet of buses.
"The crisis in Makati is over. This has been a triumph for democracy"
--President Gloria Arroyo
Among those set free was the Australian ambassador Ruth Pearce.
The United States rallied behind the besieged Philippines president and condemned the coup attempt.
“No one should be under any doubt that we fully support the legitimate civilian government of President Gloria Macapagal Arroyo,” a State Department spokeswoman said.
The rebels took over the complex of high-rise blocks and shopping centres shortly after Arroyo accused the soldiers on television of attempting a coup.
A rebel spokesman denied the group was trying to stage a coup.
“We mean no harm to anyone. We are putting these bombs to defend ourselves,” he said, accusing the government of trying to silence them.