Nobody was hurt, and members of the Islamic Centre of Escondido were able to extinguish the small blaze before firefighters around 3.15am.
The incident was being investigated as arson and a possible hate crime, said police in the city about 48 kilometres north of downtown San Diego.
A note was found in the parking lot referencing the shootings this month that killed 50 people at mosques in Christchurch, New Zealand, police lieutenant Chris Lick said. He did not elaborate about the contents of the note.
Investigators did not release information about a suspect.
