Police said no one was hurt in either of the two explosions.
The first blast was around 3 a.m. near the San Miguel Corp. main office in Manila's Mandaluyong suburb.
The second was at 4:50 a.m. in front of the Puregold Supermarket along Commonwealth Avenue in Quezon City.
A security guard said a man threw a plastic bag containing the explosive then fled.
"A man threw a plastic bag and ran off, leaving his shoes behind," security guard Darwin Taringding told police.
Police Chief Supt. Benjardi Mantele has ordered a full investigation into the incidents.
Mantele said the explosions were relatively weak.
Police are looking into a possible connection between Monday's blasts and similar predawn explosions that hit two building in Quezon City and Pasig City on Oct. 30.