Herrion, a 6-foot-3, 310-pound guard, was on the field for San Francisco's 14-play, 91-yard drive that ended with a touchdown with two seconds left.
Players had finished listening to coach Mike Nolan address them in a postgame meeting when Herrion collapsed. Medics administered CPR on him and took him to an ambulance that rushed him to a nearby hospital.
About three hours later, 49ers spokesman Aaron Salkin confirmed that Herrion had died. The cause of death was not immediately known.
"This is a colossal tragedy for the 49ers and the entire NFL community," Salkin said. "We still do not know all the details. Our thoughts and prayers are with the Herrion family."
The cause of Herrion's death cannot be determined until toxicology tests are performed. A coroner says that process usually takes three to six weeks.
The death comes a little more than four years after offensive lineman Korey Stringer of the Minnesota Vikings died of heatstroke during a training camp practice on a day during which the heat index soared to 110.
Since Stringer's death, NFL teams have increased their efforts to teach players about hydration and how to manage the heat. They have been experimenting with sensors to measure players' core body temperatures, although those by themselves wouldn't be able to prevent a heat-related death.
On Saturday night in Denver, temperatures were in the mid-60s with 50 percent humidity, although experts say heatstroke can occur even in cool conditions.
After the game, Nolan said he had no comments about San Francisco's 26-21 loss to the Broncos.
"There are more important things on our mind than the game," he said. "Right now, our thoughts and prayers are with Thomas Herrion."
Shortly after that statement, the Niners got dressed and boarded buses that took them to the Denver airport for their flight back to California.
"We didn't see anything happen," Niners defensive lineman Marques Douglas said. "I sat by my locker and prayed for him."
Herrion, a first-year player with the 49ers, played college ball at Utah and spent part of last season on the San Francisco and Dallas practice squads. He also played this season with the Hamburg Sea Dogs of NFL Europe.
Stringer's death was thought to be the first of its kind in the NFL. In 1979, St. Louis Cardinals tight end J.V. Cain died of a heart attack during training camp. Chuck Hughes, a wide receiver for the Detroit Lions, died of a heart attack Oct. 24, 1972, during a game in Detroit against the Chicago Bears.
In April, Arena Football League player Al Lucas of the Los Angeles Avengers died of a spinal-cord injury he endured while making a tackle.