The woman, identified as a call center agent, was declared dead at the Makati Medical Center, where doctors said she died of shrapnel wounds to the head and the back of her body, ABS-CBN News reported.
At least 14 others were injured Tuesday in the blast from a bomb planted in the bus, the Philippine Star reported quoting police. The incident occurred as the bus was traveling in the capital's financial district.
ABS-CBN News said the device may have been planted under one of the seats.
No one had yet claimed responsibility for the incident but the Star said police have not ruled out terrorism.
The report said the explosion was so powerful it tore a hole in a nearby perimeter wall after ripping through the bus.
Philippine President Benigno Aquino III was quoted as saying investigators should focus on the "terror aspect."
"This is a well-planned and deliberate act to kill innocent people and to sow fear among the civilian populace," Interior Secretary Jesse Robredo said.
The United States and some other Western countries have issued travel alerts for their citizens travelling in the Philippines, where the Abu Sayyaf terror group has been active.