At the time, about 20 people were performing Subuh prayers at the Surau Al-Huda, it said.
Two men on a motorcycle had hurled a beer bottle, modified into a Molotov cocktail, into the surau compound and fled.
The bottle broke into flames near the surau entrance.
Petaling Jaya district police chief ACP Mohd Zani Che Din said nobody was injured in the incident which is being investigated under Section 435 of the Penal Code for mischief by fire or explosive substance.