Wukan, in southern Guangdong province, has come to symbolise the anger felt over land seizures by rural officials.
It ousted local officials three months ago and won the right to elections as part of a deal to end unrest there.
Respected elder Lin Zuluan was voted in as village chief, with Yang Semao his deputy.
After his landslide victory, with 6,205 votes on an 80% turnout, Mr Lin said: "With this kind of recognition from the villagers, I'll work doubly hard for them."
Some 6,800 residents had turned up at a local school to cast their ballots.
Five other seats on the village committee will be filled in a run-off vote on Sunday.
Activists from other parts of the country had travelled to Wukan to observe the polls and to try to highlight their own grievances.
"Wukan is an example for us," Hua Youjuan, a village chief from Huangshan in eastern China where residents have also protested against corruption, told Reuters.
"What Wukan has achieved through its solidarity is something we can also learn from," he added.
Protests had been simmering in Wukan since September.
Villagers said officials had sold off their land to developers and failed to compensate them properly.
The unrest escalated after the death of a village negotiator in police custody in December.
Police say he died of a "sudden illness", but his family say he was beaten to death.
The granting of elections was seen as a surprising concession from the Guangdong authorities, led by ambitious Communist Party head Wang Yang.
Thousands of people turned out to elect a new leader in a Chinese village that staged a high-profile revolt over perceived local corruption.