The car was stolen from outside the Congregation Agudath Sholom of Flatbush, at 3714 18th Ave., near Coney Island Avenue, about 6 p.m., cops said.
The thief swiped the driver's keys and wallet, which had been left somewhere in the synagogue, police said.
It's unclear if the thief was aware the Torah was inside the car when he or she stole it.
"If his car was stolen and that was it, it's one stolen car out of many," said Acting President Walter Rosenblatt. "But getting back that Torah is a big deal.
"Maybe if we can get some publicity that this is gone, the person hopefully returns it," he added.
The victim, who works at the synagogue, lost other personal items, including some credit cards and articles of clothing that were stored in the car, cops said.
Anyone with information about the incident should submit a tip at NYPD Crime Stoppers or call 800-577-TIPS.