Singaporeans chanted Lee's name as the former prime minister's coffin, draped in the red-and-white national flag and protected by a glass case atop a two-wheeled gun carriage, emerged from parliament pulled by a ceremonial Land Rover.
Four F-16 fighters from the air force's Black Knights aerobatic team staged a fly-past - with one peeling off to symbolise a "missing man" - as the cortege made its way through the adjacent civic square where Lee was first sworn in as prime minister in 1959.
He kept the position for 31 years, ruling with an iron fist to transform Singapore from a sleepy British colonial outpost into a gleaming metropolis that now enjoys one of the world's highest standards of living.
Singapore became a republic in 1965 after a brief and stormy union with Malaysia. Lee died less than five months before the island celebrates its 50th anniversary as a nation.
A 21-gun salute is normally reserved for sitting heads of state but an exception was made for Lee, whom many regarded as the de facto national hero of Singapore even when he was alive.
People wept openly, waved flags and threw flowers on the street as the motorcade drove through districts associated with the political career of the British-trained former trade union lawyer.
Officials said more than 450,000 people had paid their last respects to Lee, who died on Monday in hospital aged 91, by the time his public wake ended in parliament on Saturday night.
"It has been a deeply moving experience," his son, Prime Minister Lee Hsien Loong, said on Facebook in a thank-you message to the people before the funeral ceremonies got under way.
Strangers huddled together under umbrellas as they waited patiently along the procession route which ended at the National University of Singapore, where a state funeral started with world dignitaries including Australian Prime Minister Tony Abbott in attendance.
Former US president Bill Clinton will lead the American delegation that also includes former secretary of state Henry Kissinger, a close friend of Lee.
Japanese Prime Minister Shinzo Abe, South Korean President Park Geun-Hye, Indian Prime Minister Narendra Modi, Indonesian President Joko Widodo, Malaysian King Sultan Abdul Halim Mu'adzam Shah and Brunei's Sultan Hassanal Bolkiah are among the leaders listed to attend the funeral.
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