The violin was crafted by Nicolo Gagliano in the 1760s and is valued at A$239,000.
It was gone from the trunk of Sabina Nakajima's car when she fetched it from a tow yard on Wednesday, the woman told police.
Gagliano studied under legendary violin maker Antonio Stradivari.
The instrument was on loan to Nakajima, who is a 23-year-old conservatory of music student, she said.
"I've always left my violin in the trunk and it has always been fine," Ms Nakajima said. "God knows what I was thinking this time."
Ms Nakajima had parked her car illegally, then returned hours later to discover it was towed, said Maria Oropeza of the San Francisco Police Department.
Ms Nakajima reported that her handbag, iPod music player and the violin were missing when she picked up her car, Officer Oropeza said.
The owner of the San Francisco violin shop that lent Nakajima the instrument likened the notion of a thief selling Gagliano's creation to a crook trying to discretely hawk the Mona Lisa.