The Flying Dinosaur holds riders in a prone position, to simulate being hauled off by a pteranodon.
Staff guided stranded passengers to safety through a passageway along the rail of the roller coaster.
All of the riders were evacuated safely, with no injuries reported, according to a park spokesman.More news: CervicalCheck boss steps down amid smear test blunder
The park operator said it has replaced the faulty motor control part that caused the incident, NHK reported on Wednesday.
The Flying Dragon attraction is one of the latest additions to the Universal Studios Japan, boasting the world's longest track and the farthest initial drop, according to the theme park's website. Many park-goers were undeterred by the incident and queued up to take the ride as soon as operations resumed shortly after 7 pm on Tuesday.
The ride promises to deliver an "over-the-top, thrilling experience"-a far cry from the "slowest rollercoaster" that derailed and stopped mid-ride at the Arakawa Amusement Park in Tokyo in March, which passengers hardly noticed".
"It's already a terrifying ride, so I want them to operate it safely", added a 24-year-old woman from the city of Kumamoto, who was on the rollercoaster shortly before the incident.