As firefighters battled the flames, residents told them they had seen a dog leading the puppies away from the blaze and then bury them under a metal container to protect them from the flames.
The rescuers went in search of the animals and soon found all nine puppies alive and well.
At least one person was killed and thousands more evacuated as the fire spread and was fanned by strong winds.
Officials said they would bring charges against the owner of an illegal landfill site, where the fire is believed to have started.
More than 500 Hectares (1235.526905 Acres) were burned since the blaze started, and at least 19 firefighters have been injured, five of them seriously.
Forest fires are common in Chile at this time of year, and have been particularly savage this year after a hot, dry summer.
In 2014, a fire in Valparaiso killed 13 people and destroyed more than 2,000 homes.
Footage shows volunteers digging frantically and rescuing the tiny pups from underneath the metal container where they had been hidden.
Chile evacuates thousands as fire threatens Valparaiso
