The thumping win by Anies Baswedan in the bitterly fought election for Jakarta governor signals twin threats to Indonesia’s President Joko Widodo - from rising Islamism and the renewed clout of Indonesia’s old political and business elites.

Baswedan thanked supporters after taking a decisive lead in the unofficial count on Tuesday afternoon, but not before his political patron, Prabowo Subianto, claimed victory first - thanking the scions of Indonesia’s establishment by his side.

"Our focus is social justice, ending inequality and our commitment is to safeguard diversity and unity,” Baswedan said.

The conciliatory tone contrasted with the fractious nature of a campaign that challenged Indonesia’s religious and ethnically tolerant traditions, and comments made by Baswedan on the eve of the election.

Baswedan compared the poll to the Battle of Badr, a pivotal fight in the early days of Islam that consolidated the Prophet Muhammad’s power, a win ascribed to divine intervention.

FRINGE BECOMES A FORCE

The Jakarta election was marked by the blasphemy trial of Baswedan's rival, Basuki Tjahaja Purnama, who allegedly mocked a verse in the Koran used by his opponents to claim Muslims could not vote for anyone with different religious beliefs.

Purnama is a Christian and ethnic Chinese in the world's largest Muslim-majority nation.

Huge, well-funded anti-Purnama protests in November and December sunk his high approval ratings. They were organised by hitherto fringe Islamists drawn from violent vigilante groups and Salafists influenced by Saudi Arabia’s puritanical brand of Islam.

Conservative clerics took the anti-Purnama message to the mosques throughout the campaign, said Eva Kusuma Sundari a senior official in Widodo’s party, the Indonesian Democratic Party of Struggle.

“This is a major defeat for us. The landscape is changing and it’s not favourable to us,” she said.

"We have to figure out our own understanding of this political religion without giving up our constitutional and nationalistic approach."

Tim Lindsey, an Indonesia analyst from the University of Melbourne, said Islamist groups had “emerged from the fringe to become a force”.

“This is a rehearsal for [the 2019 presidential election] and it sends a very clear message that if you play the Islam card it’s going to help you,” he said.

“If groups like these can get hundreds of thousands on the streets, you are going to want to use that power.”

Slamet Maarif, a spokesman for the Islamic Defenders Front, one of the main forces behind the push to prevent a Christian from leading Indonesia's Muslim majority capital, said the group was already eyeing the 2019 poll.

"We will maintain the existing unity of Muslims. And we will prepare Muslim unity for 2019," he told Reuters.

SUHARTO'S ELITES

Widodo, who grew up in a shack by a river in rural Java and became a successful furniture seller before entering politics, was the insurgent candidate who defeated Prabowo in the 2014 presidential election.

Popularly known as Jokowi, he became the first Indonesian from outside the elites to assume the country’s highest office.

He was catapulted to national prominence after becoming governor of Jakarta, with Purnama serving as his deputy.

His fit-and-start reform agenda has antagonised some in the business establishment who chafe against his calls for more foreign investment and increased competition in some sectors of the economy.

Among those standing alongside Baswedan and Prabowo as they claimed victory were moguls Aburizal Bakrie, Hashim Djojohadikusumo and Hary Tanoesoedibjo. All were prominent businessmen with links to the three-decade authoritarian regime of Suharto before he was ousted from power in 1998 during the Asian financial crisis.

Tanoesoedibjo, who is President Donald Trump's business partner in two resort developments in Indonesia, once worked for Suharto's son, Bambang Trihatmodjo.

Bakrie is a former chairman of the Golkar Party, which Suharto created as the parliamentary rubber stamp for his 32-year hardline rule. His family conglomerate, Bakrie Group, is prominent in the mining industry, oil and gas, and property development.

Prabowo, a former general and son-in-law of Suharto, was banned from entering the United States over his alleged human rights abuses as a military commander tasked with disrupting the student protests that eventually toppled Suharto and ushered in Indonesia’s democratic era. Djojohadikusumo is Prabowo's younger brother. Their father, Sumitro Djojohadikusumo, was the architect of Suharto's economic plans.

Considered a spent force after his defeat in 2014, Prabowo now has a platform to raise money and increase his profile ahead of another tilt at the presidency in 2019, said Wimar Witoelar, a political analyst and former presidential spokesman.

“[Baswedan] will be indebted,” he said. “The Jakarta government will be a pawn in the political play for 2019.”