Salvadorans on Sunday elected Nayib Bukele, the popular former mayor of San Salvador, as the Central American country's new president — a result that ends the near 30-year grip on power of its two largest parties.

The country's Supreme Electoral Tribunal (TSE) awarded him 53.78 percent of votes with 87.67 percent counted — a lead it considered "irreversible".

The 37-year-old president-elect, of the conservative Grand Alliance for National Unity (GANA) party, wore jeans and a leather jacket as he celebrated with supporters — thousands chanting his name and waving flags in the capital's central Plaza Morazan.

"It's a victory for the Salvadoran people; today we won in the first round and we have made history," said Bukele, who despite being a firm favorite was expected to face a second round of voting.

He has promised to increase investment in education and fight corruption — but his main task will be to confront insecurity in a country ravaged by gang violence.

He will also have to form an alliance with the rightwing opposition, which dominates congress, and govern with them until at least 2021 when the next legislative elections are held.

Bukele's opponents — Carlos Calleja of the right-wing Nationalist Republican Alliance (ARENA), and Hugo Martinez of the leftist Farabundo Marti Front for National Liberation (FMLN) — quickly recognised the win. For nearly three decades, their parties have had a firm hold on Salvadoran politics.

"We recognize the results of these elections. We are going to call the president-elect to wish him luck in facing the challenges in this country," said Calleja, the runner-up with 31.62 percent of votes. The FMLN's Martinez took third place with 13.77 percent.

Meanwhile, Organization of American States (OAS) secretary general Luis Almagro congratulated Bukele on Twitter.

"We congratulate @nayibbukele for his historic victory in the first round. We celebrate his proposal for a new chapter for El Salvador. And we salute the political matuirty of the contending candidates in accepting his victory," Almagro said.

Some 5.2 million people participated in the election, according to the elections authority chief Julio Olivo.

Voters formed long lines outside polling stations in parts of San Salvador, where gang violence and insecurity are endemic. El Salvador is among the world's most violent countries with a murder rate of 51 per 100,000 citizens.

Some 23,000 police officers and 15,000 soldiers were deployed to protect the sixth presidential election since democracy was restored in 1992 — after 12 years of bloody civil war between state security forces and leftist guerrillas.