Beltrame said he was told the club had been filled far beyond its capacity during a party for students at the university's agronomy department.
Survivors, police and firefighters gave the same account of a band member setting the ceiling's soundproofing ablaze, he said.
"Large amounts of toxic smoke quickly filled the room, and I would say that at least 90 percent of the victims died of asphyxiation," Beltrame told The Associated Press by telephone.
"The toxic smoke made people lose their sense of direction so they were unable to find their way to the exit. At least 50 bodies were found inside a bathroom. Apparently they confused the bathroom door with the exit door."
In the hospital, the doctor "saw desperate friends and relatives walking and running down the corridors looking for information," he said, calling it "one of the saddest scenes I have ever witnessed."
Rodrigo Moura, identified by the newspaper Diario de Santa Maria as a security guard at the club, said it was at its maximum capacity of between 1,000 and 2,000, and partygoers were pushing and shoving to escape.
Santa Maria Mayor Cezar Schirmer declared a 30-day mourning period, and Tarso Genro, the governor of the southern state of Rio Grande do Sul, said officials were investigating the cause of the disaster.
The blaze was the deadliest in Brazil since at least 1961, when a fire that swept through a circus killed 503 people in Niteroi, Rio de Janeiro.
Sunday's fire also appeared to be the worst at a nightclub since December 2000, when a welding accident reportedly set off a fire at a club in Luoyang, China, killing 309.
In 2004, at least 194 people died in a fire at an overcrowded nightclub in Buenos Aires, Argentina. Seven members of a band were sentenced to prison for starting the flames.
Several years later, in December 2009, a blaze at the Lame Horse nightclub in Perm, Russia, killed 152 people after an indoor fireworks display ignited a plastic ceiling decorated with branches.
Similar circumstances led to a 2003 nightclub fire that killed 100 people in the United States. Pyrotechnics used as a stage prop by the 1980s rock band Great White set ablaze cheap soundproofing foam on the walls and ceiling of a Rhode Island music venue.
The band performing in Santa Maria, Gurizada Fandangueira, plays a driving mixture of local Brazilian country music styles. Guitarist Martin told Radio Gaucha the musicians are already seeing hostile messages.
"People on the social networks are saying we have to pay for what happened," he said. "I'm afraid there could be retaliation".