The state funeral on Tuesday will be shown on giant video screens at a nearby park.
Hillary's coffin was covered with flowers and a mountain axe as the local Nepali community placed cream-coloured prayer scarves and a flower garland over a big portrait of him.
His wife, June, and son, Peter, were joined at the church by political leaders including Helen Clark, New Zealand's prime minister, who said the whole country was mourning his passing.
"New Zealand has lost its greatest hero," Clark said outside the cathedral.
Wreaths in memory of the man known to most in the country as simply "Sir Ed" were also laid by a representative of Queen Elizabeth II, the British monarch and New Zealand's head of state.
Al Jazeera's Dan Nolan, reporting from Auckland, said hundreds of mourners queued up patiently for hours for a chance to bid farewell to Hillary.
"I think we'll remember him as a great humanitarian, great role model, someone for all to be proud of," said
Paul Osborne, a mourner who had lined up in the rain to pay his respects.
Manohar Shrestha, president of New Zealand Nepal Society, praised Hillary for his charity work.
May 29, 1953 - Becomes the first person, at the age of 33, to scale the 8,850-metre Everest with Sherpa partner Tenzing Norgay
June 6, 1953 - Knighted by Britain's newly-crowned Queen Elizabeth II
1957 - Helps to set up Scott Base, New Zealand's southern-most outpost in Antarctica
1958 - Leads the first team to reach the South Pole using motorised vehicles
1962 - Establishes Himalayan Trust to help communities in the Everest region
1975 - Wife and daughter die in an aircraft accident in Nepal
1977 - Hillary's son, Peter, joins him in jet boat expedition to the source of Ganges River in the Himalayas
1985 - Aged 66 Hillary becomes first man to stand at both poles and Mount Everest after landing at the North Pole with Neil Armstrong, the first man on the moon.
1985 - Sent to India as New Zealand's high commissioner
1990 - Becomes the only living New Zealander to be featured on a banknote, the same year Peter scales Mount Everest
2003 - Nepal grants Hillary honorary citizenship marking 50th anniversary of Everest climb
2007 - Returns to Scott Base in Antarctica to mark the facility's 50th anniversary
"It is a very, very sad moment in Nepal," he told Al Jazeera. "We've lost a great leader. He was a great inspiration for all Nepalese and the world.
"Now we have many doctors, engineers from the Sherpa community and that is a big contribution."
Nepali Sherpas have staged several memorial ceremonies in Kathmandu since Hillary's death on January 11, lighting butter lamps and offering special Buddhist prayers for his reincarnation.
A former beekeeper, Hillary leapt to prominence after scaling the world's highest peak in 1953 with Nepalese Sherpa, Tenzing Norgay.
Thousands of mourners are expected to attend the funeral including descendants of Norgay, who partnered Hillary to summit the 8,850-metre peak.
Norgay himself died in 1986.
Following the historic climb, Hillary spent most of his energy helping Nepal's Sherpa people who live in Everest's shadow.
His Himalaya Trust raised about $250,000 a year, building 26 schools, two hospitals, an airport and providing scholarships for Sherpa children in the region which is home to eight of the world's 14 highest mountains including Everest.
Source: Al Jazeera and agencies