Dressed in his favorite blue navy blue suit and a blue striped shirt, Niemeyer was embalmed in Rio early Thursday before being flown here.
A solemn memorial ceremony was held in the Planalto presidential palace in Brasilia, the futuristic capital he helped created.
Afterwards, his casket, draped in the green and yellow Brazilian flag, was loaded onto a firetruck ahead of a flight back to Niemeyer's native Rio for a private wake by family and friends.
Early Friday, the body will lie in state before the burial at the Sao Joao Batista cemetery in Rio's Botafogo district.
Soon after Niemeyer's death was announced, President Dilma Rousseff hailed him as "one of Brazil's geniuses" and a "revolutionary who "always dreamt of a more egalitarian society."
Tributes poured in from abroad as well, with fellow winners of the Pritzker prize, likened to architecture's Nobel, remembering Niemeyer as a colossus in his field and his flare for wavy, curvaceous structures as a source of inspiration and creativity.
UN Chief Ban Ki-moon hailed him as "a towering figure" noting that he was one of the original architects of United Nations Headquarters in New York.
Foreign ministers of the Mercosur regional trade bloc, who gathered in Brasilia ahead of summit on Friday named him "an illustrious Mercosur citizen".
From Europe, British architect Norman Foster led tributes, remembering Niemeyer as an inspiration for himself and a generation of architects and said meeting him last year in Rio was like meeting one's hero.
British architect and fellow Pritzker laureate Richard Rogers described Niemeyer as "one of the last great modern masters, alongside Frank Lloyd Wright and Le Corbusier."
"He was an artist and poet and concrete was his natural material, allowing him to interpret his designs and free flowing ideas," added Rogers, who designed Paris' Pompidou Center museum.
In France, Communist Party leader Pierre Laurent eulogized Niemeyer as "an extraordinary man who was able to ally his creative talent to his commitment to Communism throughout his life."
The architect, whose typically wavy design for the party's headquarters in Paris is considered one of his outstanding works, spent many years living in France while Brazil was under military rule.
French Culture Minister Aurelie Filippetti expressed thanks for the 20 plus original buildings that the Brazilian icon, a long-time collaborator of Le Corbusier, bequeathed to France.
Winner of the Pritzker Prize in 1988, Niemeyer started his career in the 1930s and went on working well into the 21st century, after turning 100.
Niemeyer works can be found in countries as far-flung as Algeria, Italy, Israel, the United States and Cuba, whose longtime revolutionary icon Fidel Castro was one of his personal friends.
The Cuban communist party newspaper Granma called Niemeyer an unwavering friend of the Cuban revolution and of Castro.
It quoted Niemeyer as saying once, "I will never shut my mouth. I will never hide my Communist convictions."
In a show of his support for Cuba and opposition to the US embargo against it, when Castro turned 80 in 2006 Niemeyer gave Cuba a sculpture: an open-mouthed monster facing off against a Cuban holding his country's flag of blue and white stripes with a red triangle enclosing a star.
In 1956, Niemeyer was appointed chief architect on a project to provide Brazil with a modern new capital city in the heart of the jungle.
One of his most spectacular works was a contemporary art museum created in 1996 -- when Niemeyer was already 89 years old.
Located in Niteroi, a town near Rio, it includes an structure shaped like an upturned dish, poised over the ocean on rocky cliffs.
Born in Rio into a middle class family of German, Portuguese and Arab ancestry, Niemeyer created some 400 buildings in all, including the Serpentine Gallery in Hyde Park, London and the Penang State Mosque in Malaysia.
In 1928, he married Annita Baldo. The marriage lasted 76 years until Annita's death in late 2004. Their only daughter, Anna Maria Niemeyer, died of emphysema in 2009 at the age of 82.
At the age of 98, the star architect got married again, this time to his loyal assistant Vera Lucia Cabreira, 38 years younger than him.
"I accompanied him to the hospital a month ago. I saw him get better and get worse. He was lucid, told me he wanted to eat cake and have coffee," Globo's news portal G1 quoted her as saying.
The jury that awarded Niemeyer the Pritzker prize wrote: "he captured the essence of Brazil with his architecture. His buildings distilled the colors, light and sensual image of his native country."