She will be buried next to her husband at Manila's memorial park later on Wednesday.
Aquino died on Saturday at the age of 76 from colon cancer.
Rivals pay respect
|The family of former dictator Ferdinand Marcos paid their respects [Reuters]
Ahead of the funeral her body lay in state in the cathedral where mourners including political rivals and even former military commanders who had plotted coups against her, had lined up to pay their respects.
"Her aura was her armour. You couldn't possibly hurt her," said retired navy commodore Rex Robles, who as a young colonel was among a group of officers who sought to topple Aquino in the late 1980s in one of seven attempted coups during her presidency.
Another former coup leader, Brigadier-General Danilo Lim, who as a captain joined one of the bloodiest attempts to oust Aquino in 1989, said that while he had "an uneasy history" with her as president, she would be remembered as a "guiding light" of democracy.
Early on Wednesday Gloria Arroyo, the current president, arrived at the cathedral to pay her respects despite a long-running political rivalry with the Aquino family.
Benigno Aquino III, the former president's son and an opposition senator, had said he would not prevent Arroyo from attending the wake, but added "if they think we will leap for joy just because Mrs Arroyo is visiting - well, it won't be that way".
In recent years Aquino had been sharply critical of Arroyo, calling on her to resign over allegations of corruption and vote fraud.
|Thousands of Filipinos are expected to line the route for the funeral procession [Reuters]
The Aquino family had earlier asked the government to break with protocol and not hold a state funeral for Aquino, avoiding awkward scenes such as having her body lie in state in the presidential palace where Arroyo works.
Also paying respects to Aquino ahead of Wednesday's funeral were the son and daughter of Marcos.
House of Representatives member Ferdinand Marcos Junior and elder sister Imelda "Imee" Marcos joined the wake on Tuesday afternoon, shaking hands with one of Aquino's daughters, Maria Elena Cruz.
Aquino had always blamed the late dictator Marcos for the 1983 assassination of her politician husband Benigno Aquino at Manila airport on his return from US exile to lead the opposition against Marcos.
The political upheaval unleashed by the murder marked the beginning of the end of Marcos's rule.
Amid widespread street protests in 1986 that became known as the "People Power" uprising, he eventually fled into exile, bringing Benigno Aquino's widow, Corazon, to the presidency.