Indonesian militias deployed terror tactics to intimidate people into voting for continued union, but Timor-Leste voted overwhelmingly to split from Indonesia.
President Joko Widodo, in a televised speech announcing Habibie's death, described Habibie as a "world-class scientist and the father of technology in Indonesia".
Indonesian soldiers carry the picture and casket of Habibie during his funeral ceremony at Kalibata Heroes Cemetery complex in Jakarta, Indonesia.
Countless numbers of mourners lined the streets of the funds, Jakarta, to look at the motorcade carrying the entire body of Indonesia's 3rd president to the Kalibata heroes' cemetery.
Habibie had been treated on the intensive care unit of the Gatot Subroto Army Hospital since 1 September 2019, reportedly for heart failure.
Malaysian politician Anwar Ibrahim paid tribute to Habibie as "family", recalling the Indonesian's support during his years in prison.
In January 1999, Habibie said East Timor could have independence if its people rejected autonomy within Indonesia. His wife of 48 years, Hasri Ainun Habibie, a medical doctor, died in 2010. It ended just after only 17 months in Oct 1999 when he withdrew from competition in presidential elections.
Habibie was a trained aerospace engineer who had been working in Germany for almost two decades when then-President Suharto convinced him to come back home in 1974 and lead an effort to industrialize Indonesia's economy.
Habibie became the science and technology minister and used his proximity to Suharto to pursue pet projects, including a state aircraft maker, a steel refinery and various defense-related industries.
Though he was a product of Suharto's "New Order" administration, which gave a strong political role to the military and stifled opponents, Habibie oversaw democratic reforms to free political prisoners and allow press freedom.
"Not only Indonesian men and women shed him, but we also lost him", East Timor Prime Minister Taur Matan Ruak wrote on Twitter.
"Malaysia regards former president BJ Habibie as Malaysia's closest friend and his passing is a huge loss for the region". Habibie was born in June 1936 in a small town in South Sulawesi, and studied aviation and aerospace engineering in Germany and the Netherlands before returning home in the mid-1970s. They are survived by two sons, neither of whom are involved in politics.