They came from around the country, by train, plane, car and even on foot, chanting Bhutto slogans, some wailing and beating their chests in an outpouring of emotion, the BBC's Barbara Plett reports.
Mourners kissed her grave and laid flowers at the mausoleum, where official ceremonies were delayed because the site was shrouded in winter mist and fog for much of Saturday morning.
These were her devoted supporters, but many other Pakistanis were also feeling the loss of the charismatic politician, famous abroad and at home, our correspondent says.
Prime Minister Yusuf Raza Gilani paid tribute in a televised address, saying Mrs Bhutto had "worked for poor segments, for poor people and she was the only ray of hope for the people of this country, she was a hope for the region".
Mr Zardari delivered a televised speech from the family home in Naudero, Sindh.
"Dialogue is our biggest arsenal," he said.
"The solution to the problem of the region... is politics, is dialogue and is democracy in Pakistan.
"I want to tell the oldest democracy and the largest democracies of this world: listen to us, learn from us. We have lost our people, we do not talk about war, we do not talk about vengeance."
Thousands of police officers have been deployed in Garhi Khuda Bakhsh, amid fears that Mr Zardari could also be targeted during his visit to the mausoleum.
Eulogies to Bhutto gloss over her mixed record when in power and her controversial decision to make a deal with Pakistan's military leader, Gen Pervez Musharraf, in order to return from exile, our correspondent adds.
Many Pakistanis say they sorely miss Benazir Bhutto
But her assassination by suspected Islamist militants shook the nation to the core and although Bhutto's Pakistan People's Party and her husband swept to power in the wake of her death, there is still a feeling she left a vacuum that has not been filled, she says.
Pakistanis are missing her political experience and international stature, as they face crises ranging from a raging Islamist insurgency to dangerous tensions with India, our correspondent notes.
Pakistan has redeployed some troops from the north-west to strengthen its border defences, while India has advised its citizens against travelling to Pakistan.
On Friday, the UN secretary general expressed hopes that a UN investigation into Mrs Bhutto's assassination could be set up in the near future and said he was committed to helping Pakistan's search for "truth and justice".
Earlier this year, British detectives investigating the fatal attack in Rawalpindi said Mrs Bhutto had died from the effect of a bomb blast, not gunfire.
Their account matched that of the Pakistani authorities.
But Bhutto's party has insisted she was shot by an assassin and accused the government of a cover-up.
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