As people across the Catholic nation woke to the news of the 76-year-old's death, President Gloria Arroyo declared a 10-day period of mourning for Aquino, whom she praised as a "national treasure."
Aquino's family announced her death early Saturday.
"Our mother peacefully passed away at 3:18 am, August 1, 2009 of cardio-respiratory arrest," Senator Benigno Aquino Jr, said in a statement outside the Makati Medical Centre in Manila, where his mother had been hospitalised.
"She would have wanted us to thank each and every one of you for all the prayers and the continuous love and support," he said.
"It was her wish for all of us to pray for one another and for the country," he added.
Arroyo, in the United States on an official visit, said: "Aquino led a revolution that restored democracy and the rule of law to our nation at a time of great peril."
Former aide and press secretary Teodoro Locsin, who is also a close family friend, openly wept on television.
"The purity, the nobility, never failed. She never asked for anything," in return, Locsin said.
He said more than anything else, the former leader removed the "centre of corruption in government, because she would not be corrupt."
US President Barack Obama "was deeply saddened" by Aquino's death, read a statement from White House Press Secretary Robert Gibbs.
"Her courage, determination, and moral leadership are an inspiration to us all and exemplify the best in the Filipino nation," the statement said.
Tributes also came from the governments of fellow Southeast Asian countries Indonesia, Singapore and Thailand, as well as Japan and the European Union representative in Manila.
China called the late democracy figure "a good friend" while Pope Benedict XVI hailed her as "courageous" and as a "woman of deep and unwavering faith".
Aquino's five children have opted to bury their mother in a private ceremony next week, and said they have not talked with any representatives from Arroyo's office.
In a solemn ceremony, her casket draped in the national colours was received by a military honour guard at a Catholic school where the public will be allowed to pay their last respects.
Weeping family members and close friends showered her coffin with yellow confetti.
She will be laid to rest beside her husband, Benigno "Ninoy" Aquino at a private cemetery on Wednesday next week, the family said.
In Manila's Makati financial district, huge posters of Aquino were displayed while neighbours left flowers at the family home. Requiem masses were held in Catholic churches nationwide.
Former first lady Imelda Marcos said her family joined the nation in mourning and praying for Aquino. She had earlier said she didn't bear Aquino any grudges, and would have visited her in hospital if she had been allowed.
A former housewife who reluctantly became president, the soft-spoken Aquino rewrote the country's constitution, freed all political dissidents jailed by Marcos, and initiated peace talks with insurgent groups.
Problems in her coalition later emerged, and Aquino survived a series of bloody coup attempts by the same forces that went against Marcos.
"I realised that I could have made things easier for myself if I had done the popular things rather than the painful but better ones in the long run," Aquino once said while reflecting on her presidency.
Until March last year, when she withdrew from public life after being diagnosed with colon cancer, she had been active in street protests denouncing government corruption.
She had also repeatedly demanded that Arroyo, a former protege whose nine-year presidency has been marred by scandals, step down.
A humble moral crusader, Aquino once famously rejected an offer of a presidential limousine to travel to the inauguration of her successor, Fidel Ramos.
Aquino later joined the Church in rallying the public in a military-backed peaceful revolt that ousted president Joseph Estrada, a self-proclaimed womaniser and former action movie star whose regime was also rife with corruption.
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