The downpour ripped a large swath out of one of 36 panels of plastic stretched above the seating in the stadium, local authorities said. Televised images showed a large triangular tear in the covering that dwarfed workers gathered around the rim of the hole to inspect it.
Though officials say the roof will be repaired before Confederations Cup games begin on June 15, the damage underscores concerns about Brazil's preparedness to host the World Cup, in 12 cities next year, and the 2016 Olympics in Rio de Janeiro.
Other major venues have also suffered problems in recent weeks as Brazil, which has invested billions of dollars in construction of new facilities, races to meet deadlines set by organizers of the events.
Much of the area around Rio's Maracanã stadium, which is one of the best-known arenas in the world and has been totally rebuilt for the forthcoming events, remains a construction site. Attendees at a re-inauguration of the stadium last month had to be bussed in from a nearby facility.
Visitors at other stadiums have complained of unfinished bathrooms, leaky plumbing and other problems that critics blame on hasty preparations.
Engenhão, another big Rio stadium which was built from scratch before the 2007 Pan-American Games and is slated to host Olympic events, is closed after inspectors discovered structural flaws in its roof. Botafogo, the club that used the stadium for home matches, has been unable to play there since March.
Brazilian officials say all stadiums and other infrastructure will be ready for the big events. In a weekly radio chat broadcast on government radio, President Dilma Rousseff on Monday expressed delight at having christened, often by kicking a ball at midfield, all six Confederations Cup venues.
"These six stadiums show that the (Brazilian) people have the determination, capacity and competence to host the best World Cup of all time," she said.
The 50,000-seat Salvador stadium, known as the Fonte Nova, has been rebuilt at a cost of 600 million reais ($293 million). Disaster struck at a previous arena on the same site in 2007, when part of the structure gave way during a match, killing seven people.
Salvador is Brazil's third-largest metropolitan area and a popular tourist attraction.