Webcor Builders senior vice president Len Vetrone said the workers are both carpenters and are in stable condition Friday.
The workers for the San Francisco-based company were installing scaffolding at 350 Mission St. when it collapsed around 2:20 p.m. Thursday, according to fire officials.
One of the workers fell 40 feet and another fell 30 feet, fire department spokeswoman Mindy Talmadge said.
They were both transported to a hospital with serious injuries, Talmadge said.
The California Division of Occupational Safety and Health is investigating the accident and the work site has been shut down during the investigation.
Vetrone said Webcor is working with Cal/OSHA on the investigation and hopes work will resume at the site on Monday.
The construction at 350 Mission St. is on a new Salesforce.com building. According to the project's website, the skyscraper will be 27 stories tall.