Former Indonesian president B.J. Habibie waves to journalists as he arrives to testify in the trial of a former military chief in Jakarta in 2003. (Achmad Ibrahim/AP)

B.J. Habibie, a former Indonesian president who allowed democratic reforms and an independence referendum for East Timor following the ouster of the dictator Suharto, died Sept. 11 at an army hospital in Jakarta. He was 83.

Mr. Habibie, Indonesia’s third president, had been undergoing treatment for heart problems, said his son, Thareq Kemal Habibie.

Mr. Habibie’s unpopular presidency was the shortest in modern Indonesia’s history but was transformative. He was tapped to lead Indonesia by Suharto as the military dictator’s 32-year hold on power crumbled in May 1998 during a student uprising and a devastating economic crash. It ended after only 16 months, in October 1999, when he withdrew from contention in presidential elections.

An engineer educated in Indonesia, the Netherlands and Germany, Mr. Habibie spent nearly two decades working for German aircraft maker Messerschmitt-Bölkow-Blohm before returning to Indonesia in 1974 to help lead Suharto’s campaign to industrialize the economy.

As president, Mr. Habibie apologized for past human rights abuses and outlined an eight-point reform program “to build a just, open and democratic society.” He ordered the release of political prisoners, dismantled restrictions on the news media and reformed politics to allow free elections.

He lifted a three-decade ban on the speaking and teaching of Mandarin as part of an easing of discriminatory policies against ethnic Chinese that was instituted by Suharto after his anti-communist pogroms of 1965-66.

Mr. Habibie in 2010. (Barbara Walton/AP)

Responding to international criticism of Indonesia’s occupation of Portugal’s former colony of East Timor, Mr. Habibie surprised Indonesians by announcing in January 1999 a plan to hold a referendum under U.N. supervision on self-determination, offering a choice between special autonomy and independence.

Indonesian militias sought to intimidate people into voting for continued union, but East Timorese voted overwhelmingly to split from Indonesia.

In 2017, the young democracy held presidential and parliamentary elections that were the first without U.N. supervision since peacekeepers left in 2012.

Despite his reforms, Mr. Habibie was unable to master the political tumult unleashed by the student uprising.

He described the bloody riots that ended Suharto’s dictatorship as “barbaric,” further alienating students who feared he was betraying their democratic revolution and staged violent protests against his presidency.

Mr. Habibie in 2007. (Achmad Ibrahim/AP)

A failure to prosecute a longtime friend over allegations of massive corruption undermined his campaign to stay in power. On Oct. 20, 1999, Mr. Habibie withdrew from upcoming presidential elections.

Parliament was already moving to elect a new head of state after lawmakers rejected his “accountability” speech on the successes and failures of his months in office.

Bacharuddin Jusuf Habibie was born in the South Sulawesi town of Parepare on June 25, 1936, and was the fourth of eight siblings.

His father was of native Sulawesi descent and his mother a Javanese noblewoman from the ancient sultanate of Yogyakarta. His wife, Hasri Ainun Habibie, a medical doctor, died in 2010. A complete list of survivors was not immediately available.