On Thursday several thousand demonstrators from factions for and against the governor fought with sticks, rocks, baseball bats and machetes.
Images of the two sides beating each other with sticks in Cochabamba's picturesque plazas were broadcast on national television.
Authorities said 1,500 soldiers had been dispatched to the city to restore order, but only small groups of troops were visible early Friday.
Cochabamba medical authorities said that the injuries from the clashes - mostly from sticks and rocks, but also from bullet wounds - had risen to 130.
The battle took place on a day when Reyes, a former presidential candidate widely considered to still harbour national ambitions, had travelled to the Bolivian capital La Paz to meet with four other governors on a political strategy opposing Morales, the Bolivian president.
Tensions between Morales and opposition governors have heightened in recent weeks, with the president proposing to sending deputies from La Paz to monitor the state governments' activities.
Opposition governors immediately threatened to send their own delegations to keep a closer eye on Morales.
Reyes joined the autonomy movement, calling for Cochabamba to hold a second vote on a referendum giving the states greater power.
The referendum was defeated in a nationwide election in July, with 63 per cent of Cochabamba voters opposed to autonomy. Reyes blamed Morales for not reacting more forcefully to protests earlier in the week.
In a televised message on Thursday night, Alvaro Garcia Linera, the vice president, confirmed two deaths in the unrest, an opposition protester and a government supporter.
He said Reyes abandoned his state during a crisis. "He left Cochabamba despite the severity of the conflict and came to La Paz to play politics, to conspire against the government, to prepare more demonstrations," Garcia Linera said.
"The duty of the governor is to be with his people, back there in Cochabamba, seeking peace, seeking solutions."