Young men in jeans or shorts and t-shirts chased the 580-kilogramme (1,280-pound) beast, named Vulcano, through the fortified town of Tordesillas in central Spain.
It was slaughtered after crossing a bridge into a meadow where it faced crowds of people, some on horseback and many carrying lances, in an ancient event condemned by animal rights defenders.
A total of 12 people were injured in the annual run, known as the Toro de la Vega, a Red Cross spokesman said.
The bull gored Armestre in the right thigh.
Armestre, who was conscious and speaking to AFP's Madrid office after the injury, was taken to a hospital in Valladolid for surgery.
The Red Cross official said Armestre's condition was serious but not life-threatening, describing the skewering as "long but not too deep, that is to say, it is not an excessively serious goring".
About 100 animal rights activists rallied in Tordesillas to protest the bull-run, waving a sign that read: "More culture, less torture."
Hundreds of activists from the Party Against Bullfighting and Animal Cruelty, had also protested in Madrid three days ahead of the event.
The group delivered a petition to Spain's parliament today, saying it contained more than 85,000 signatures calling for the abolition of the Toro de la Vega, which dates back to 1453.
Tordesillas' Socialist mayor Jose Antonio Gonzalez Poncela played down the protests, saying there were similar demonstrations at bullrings around Spain "so it is nothing more than that".
"There are always people in favour and people against in all aspects of life, not just for bullfighting," he told Spanish public radio RTVE.
