Only the Airport Express remained open as protesters began fresh demonstrations in the autonomous Chinese territory.
Chief executive Carrie Lam has defended her decision to invoke emergency powers in order to restore order.
Hong Kong had been through a “very dark night” of “extreme violence”, she said.
Unrest intensified on Friday after a young demonstrator was shot in the leg by a police officer.
Protesters have also called on people to defy a ban on face masks announced by Ms Lam.
Supermarkets and banks were also closed, reeling from Friday’s chaos when rioters targeted MTR stations and, reportedly, businesses with links to mainland China.
“The radical behaviour of rioters took Hong Kong through a very dark night, leaving society today half-paralysed,” Ms Lam said in a pre-recorded video statement.
“The extreme violence clearly illustrated that Hong Kong’s public safety is widely endangered. That’s the concrete reason that we had to invoke emergency law yesterday to introduce the anti-mask law.”
Hong Kong Protesters had set fires at stations, as well as to an empty train, and injured two staff.