Some 10 activists who had remained after the 2:00 pm deadline passed were arrested, according to the North Dakota Joint Information Center.
Earlier this month, President Donald Trump signed an executive order to revive the pipeline project. After the final permit was issued, construction on Dakota Access began almost immediately.
Native Americans and their supporters began leaving the federal land -- which was occupied by a population that swelled into the thousands at times -- singing traditional songs and banging drums.
State and tribal authorities planned to begin coordinated efforts to clean up the camp, removing garbage, structures, vehicles and other debris, in anticipation of seasonal flooding in the area.
More From This Section
Without the cleanup, the authorities said local waterways could be contaminated. More than 230 truckloads of debris had been cleared out as of Monday, officials said.
Campers burned some structures on their way out of the camp, in what they said were ceremonial rituals.
Some protesters had informed law enforcement that they would engage in passive resistance and expected to be arrested, Tom Iverson of the North Dakota Highway Patrol told local television station KFYR.
"People were free to leave," he said, adding that the evacuation was intended to "avoid an ecological disaster."
State authorities were also offering protesters bus fare to return home and hotel lodging for one night.
Native Americans and others began protesting at the camp starting last April, in opposition to the 1,886-kilometer oil pipeline. Its route runs under land the Standing Rock Sioux consider sacred and under the Missouri River, which is the source of drinking water for the tribe's reservation.