The latest crash occurred at 9:13 a.m. near the intersection of Third and King streets and involved an outbound K-Ingleside train, spokesman Paul Rose said.
Rose said that people traveling in the car refused medical treatment at the scene and that there were no reported injuries in the Muni vehicle.
Shortly after the crash, Muni began providing bus shuttles to ensure uninterrupted service in the area.
The scene was cleared by 9:50 a.m., but Rose said that Muni plans to continue the supplemental service for a short time until trains can resume normal service.
It was unclear what caused the crash, he said.
"It's too early to tell who was at fault," Rose said. "Just like the other crash, we're going to investigate the incident."
The earlier crash occurred shortly before 5:45 a.m. at the intersection of Third and 22nd streets in the city's Dogpatch neighborhood and involved a police patrol car that was broadsided by a T-Third light-rail vehicle.
The crash hospitalized the two police officers in the car, as well as the Muni operator and a female passenger in the car. All four victims' injuries are considered minor, authorities said.