An exit poll by the Indonesia Circle Institute polling agency showed rebel former foreign minister Zaini Abdullah from Partai Aceh with more than 54.4 percent. Abdullah was foreign minister for former rebel group, the Free Aceh Movement (GAM).
Former Aceh governor Irwandi Yusuf got 29.9 percent of vote, the Institute said. Yusuf stepped down as governor in February when his term ended and is running as an independent.
Official results from the Aceh Independent Election Commission are expected next week.
In the second only governor's election in Aceh, a semi-autonomous region on Indonesia's northwestern tip that has used Islamic law since insurgents fighting Jakarta's rule signed a peace deal in 2005, both sides complained of voter intimidation.
Yusuf said several campaign vehicles belonging to his team were burned by unidentified attackers.
"There is hindrance in the field, intimidation. People were scared. There were murders, kidnappings, knocking on people's doors to tell them to not vote for a certain candidate and that if they don't pick a certain candidate there will be a war," he told reporters on Monday.
At least thirteen people died in the run-up to the election in Sumatra island's poorest province, Jakarta-based risk firm Concord Consulting said in a report.
"The elections, which were delayed three times since last year, have been plagued with alleged politically motivated violence, including at least 13 murders," the report said.
Aceh shows that a guerilla conflict can be resolved by allowing rebels to take part in the political process, said security analyst Sidney Jones of the Brussels-based International Crisis Group.
One challenge for Abdullah and Partai Aceh if they win is to reconcile with supporters of other parties, she said.
"The most important issue is to show that everybody will be treated equally whether or not they were past combatants or past supporters of the Partai Aceh movement ... and that there will be serious attention to the economic and social problems of Aceh," she said.
Rebels laid down their arms after the Dec. 26, 2004, tsunami that left 170,000 dead or missing. In all, the tsunami killed about 230,000 people in 13 Indian Ocean nations.
Aceh benefited from billions of dollars of aid after the disaster and has recovered gradually, but many there are demanding more stability.
The region was plagued by the separatist conflict for three decades, including periods of military rule. Human rights abuses were rife and thousands of civilians died.
Former rebels now dominate politics and violence during the campaign was linked to the aftermath of the insurgency. The main fault lines are between Partai Aceh, formed by GAM and which controls Aceh's parliament, and Yusuf who won elections in 2006.
"What Acehnese want is peace. It's a definite prize because Aceh has suffered from 30 years of conflict," said Irfandi Djailani of Forum LSM Aceh, a consortium of non-governmental groups.
