The billionaire businessman and outgoing welfare minister was elected chairman in the early hours of the morning after a tense party congress marred by scuffles and shouting matches between delegates, Golkar officials said.
Bakrie, 62, won 296 votes compared to 240 for his closest rival, media tycoon Surya Paloh.
The youngest son of Suharto, who died last year after using Golkar to rule the country for 32 years until his downfall in 1998, launched a surprise bid for the chairmanship but failed to win a single vote.
Bakrie could not be reached for comment but he was quoted by the Detikcom news website as saying Golkar, founded in 1964, was the "vehicle of the Indonesian people to reach our shared ambitions".
The session to elect a new leader started at midnight and finished at dawn, and was held in the Riau provincial capital of Pekanbaru.
Bakrie replaces outgoing Vice President Jusuf Kalla as Golkar chief.
Kalla came a distant third in presidential polls in July, which were won in a landslide by incumbent Susilo Bambang Yudhoyono of the Democrat party.
Mattalatta laughed at the performance of Suharto's son Hutomo Mandala Putra, popularly known as Tommy Suharto, saying the 47-year-old was "not in the minds of voters".
Tommy was released from prison in 2006 after serving four years of a 15-year term for ordering the murder of a Supreme Court judge who had convicted him of corruption.
The nationalist Golkar Party was founded by Suharto and has never been in opposition, but its fortunes have waned in recent years and it garnered only 14.45 percent of the vote in general elections in April.
Bakrie's family controls a vast conglomerate including interests in palm oil, telecommunications, coal and gas.
He has been accused in the past of using his political influence to bail out his family businesses from debt, although he denies any conflict of interest between his public duties and private investments.
A Bakrie group gas drilling company has been blamed for triggering a massive mud volcano that has been devouring land and homes in East Java since May 2, 2006, causing an estimated 4.9 billion dollars in damage and killing 13 people.
The company, Lapindo Brantas, has been accused of failing to fully compensate displaced residents of 12 villages that were wiped out by the disaster.
It says an earthquake caused the mud to spew from one of its drilling wells, but independent scientists say the company was almost certainly to blame and warn that the volcano could continue to erupt for thousands of years.
Source: AFP Asian Edition