She had been suffering from colon cancer for more than a year and recently announced she was refusing further treatment.
Her family had said she was leaving her fate to God, prompting church services offering prayers for her health.
Mrs Aquino became president when the 1986 "people power" uprising deposed former dictator Ferdinand Marcos.
"Our mother peacefully passed away at 0318 [1918 GMT Friday] of cardio-respiratory arrest," Mrs Aquino's son, Senator Benigno Aquino Jr, told the media.
"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."
Mrs Aquino, who was known as Tita (Aunty) Cory, had been admitted to hospital about a month ago suffering from a loss of appetite related to her condition.
In a statement at the time, her family said they remained "in complete trust in God's infinite healing power".
"She has and always will be a woman of faith, a fighter, a source of hope and inspiration for all of us, not just her family but our entire nation as well," the statement said.
A series of daily masses were held to pray for Mrs Aquino's health, at least one of which was attended by her former political rivals, President Joseph "Erap" Estrada and former first lady Imelda Marcos.
-ICON OF PHILIPPINE DEMOCRACY, ASIA'S FIRST FEMALE PRESIDENT, THE LADY IN YELLOW, WIFE OF THE FAMOUS BENIGNO AQUINO JR.- MARIA CORAZON