The standoff, which temporarily shut down a nearby freeway as it began Wednesday morning, came to an end after a special camera sent into the room confirmed that Peter James Thomas, 38, was dead, San Rafael police said Thursday.
Police would not say how Thomas died but said it wasn't from any law enforcement action. He died sometime overnight, they said.
San Rafael police Sgt. Raul Aguilar said the girlfriend was questioned after the incident but was not under arrest.
"She was released and has gone home," Aguilar said. Police did not release her name, age or the city she was from.
Police investigating Sunday's stabbing of a clerk at a nearby supermarket tracked Thomas to the Extended Stay hotel off Interstate 580.
Shortly after the standoff began, a gunshot was fired out the window of his second-floor hotel room toward the freeway, prompting authorities to evacuate the hotel and halt traffic on a stretch of I-580, including the Richmond-San Rafael Bridge. No one was injured by the gunshot.
The bridge reopened about an hour later, but traffic remained diverted around the hotel for the rest of the day, creating commute headaches on the busy freeway. It was fully reopened after midnight after authorities placed a large steel plate outside Thomas' window to block any more bullets from endangering motorists.
During the standoff, guests of the hotel had to evacuate their rooms. They were being allowed to return to their rooms Thursday afternoon.