The deluge blocked roads and prompted an evacuation in the centre of the country amid what has been described as the worst weather front in a decade.
President Gabriel Boric visited the region over the weekend with local authorities.
“Unfortunately, two of our citizens who were trapped under fallen trees lost their lives and three missing people are being sought,” he said.
At least 419 people were left homeless and 1,002 others evacuated to safe places due to the disaster, Boric said.
Various parts of the port city of Valparaiso were also affected by the floods, he added.
Interior minister Carolina Toha announced that a “state of disaster” has been declared in Valparaiso and Biobio.
Authorities also warned residents to be careful, saying the heavy rains and risks of flooding will continue for a while.
Climate change is increasingly driving extreme weather. The rains come months after a period of wildfires and severe drought that destroyed hundreds of homes and left dozens of people dead in Chile.