The military presence was part of a state of emergency declared by President Sebastián Piñera in response to student-led protests Friday that paralyzed the city.
Protesters burned several subway stations and damaged dozens of others, and some set fire to a high-rise energy company building. Officials reported 156 police officers and 11 civilians injured and more than 300 people arrested.
The conservative Piñera vowed that those responsible for the violence "are going to pay for their deeds."
New but less rowdy protests broke out again at midday Saturday in several areas around the metropolitan area, and police fired tear gas to break some of them up.
The government recently raised subway fares from about $1.12 to $1.16 due to rising fuel prices.
The head of the subway system, Louis De Granges, said the vandalism caused hundreds of millions of dollars in damage and said it wasn't clear when service could resume. That means some 2.4 million people could have difficulties getting to work or school on Monday.
Chilean governments of left and right have been wary of bringing soldiers back into the streets since the end of a dictatorship during which thousands of suspected leftists were killed and dissent was ruthlessly crushed.
"Piñera's decision to deploy the military in Chile — a country that experienced a 17-year repressive dictatorship — is troubling and could further destabilize the situation, said Jenny Pribble, associate professor of political science at the University of Richmond. "It also sends a message to Chileans that the parties of the right still see the military, and not democratic process, debate, and dialogue, as the ultimate solution to social conflict."