The ferry, the MS San Francisco, collided with a smaller boat around 4 p.m., according to Golden Gate Transit spokeswoman Mary Currie. Currie said the boat was traveling at a high speed.
The Coast Guard responded to the scene and found that two people on board the smaller boat, a 22-foot pleasure craft, were injured, Coast Guard Lt. Mark Leahey said.
Rather than transfer the two to the Coast Guard boat, a Coast Guard crew member transferred to the pleasure boat and drove it to Sausalito.
The two injured parties were then taken by helicopter to a hospital, Leahey said.
The extent of damage to the boats is unclear, but both were able to drive away from the scene, Leahey said.
The ferry, which was carrying around 500 people, arrived at the San Francisco Terminal at 5 p.m. and headed back to Sausalito at 5:15 p.m., Currie said. It was taken out of service once it returned to Sausalito around 5:45 p.m., and another boat, the MS Sonoma, was brought in to complete ferry service for the day.
All five crew members will be drug tested and placed on administrative leave pending the results, as per standard procedure in such investigations, according to Currie.
The cause of the collision remains under investigation.