British astronaut Tim Peake, astronomer royal Martin Rees, and actor Benedict Cumberbatch, who played Hawking in a television film and narrated his documentaries, delivered addresses.
The thanksgiving service is being attended by friends and family and 1,000 members of the public who applied for seats in a ballot.
"It is a message of peace and hope, about unity and the need for us to live together in harmony on this planet", she said.
His voice will be broadcast into space after the service honoring his life.
Hawking's daughter Lucy described the music to accompany the physicist's words as a "beautiful and symbolic gesture that creates a link between our father's presence on this planet, his wish to go into space and his explorations of the universe in his mind", according to the BBC.
Hawking's passing earlier this year touched almost the entire world, including executives across Silicon Valley and other scientists, including Neil deGrasse Tyson and British astronomer and broadcaster Professor Brian Cox, who is also attending the service at Westminster Abbey. There were 25,000 applications for 1,000 available tickets.
Recent burials of prominent scientists inside Westminster Abbey include Ernest Rutherford, a pioneer of nuclear physics, in 1937, and Joseph John Thomson, who discovered electrons, in 1940. The famous physicist showed in 1974 that, contrary to popular belief at the time, black holes do in fact emit radiation. His book "A Brief History of Time" sold 9 million copies - even if many readers didn't finish it - and he appeared on "Star Trek: The Next Generation", "The Big Bang Theory" and "The Simpsons".