Eight Indians were injured, none seriously, local Dr. Luis Angel Penna said.
In an unrelated incident in the same region Wednesday, soldiers shot and killed a man when he ignored orders to halt at a military roadblock, the town's chief of security told The Associated Press.
The man was not an Indian, said the official, Carlos Pascue, but a group of Nasas angered by the killing seized 30 soldiers and held them for 10 hours before releasing them.
The retaking of the hilltop in Toribio came a day after Indians armed with clubs and rocks dragged six soldiers off it.
Members of the 115,000-strong Nasa tribe, who reject firearms and arm themselves only with wooden staffs, began mobilizing last week to insist that the military and leftist rebels leave their traditional lands.
The Indians say they are tired of being caught in the crossfire of Colombia's long-running conflict.
The government rejects the demand, and President Juan Manuel Santos tweeted Wednesday that Indians will not be allowed on military bases. His defense minister and military chief allege rebels have infiltrated the Indians' ranks.
Santos said he had authorized his interior minister to open a dialogue with the Nasa "when they cease hostilities."
The region is a corridor for cocaine smuggling and locals also cultivate high-grade marijuana.