The hostage-taker, who was armed with an M16 rifle, also died as shots were fired and police stormed the vehicle.
The gunman, a former police inspector who was fired last year, had originally seized 24 people, including the driver, in a bid to get his job back.
Nine passengers had been released before the final showdown and the driver earlier escaped through a window. He told police the gunman had started firing at passengers.
A 14-year-old boy watching the siege was wounded. Most of the passengers were from Hong Kong.
Five hostages were brought to the Manila hospital, two of them dead on arrival and three alive without injuries.
The hospital reported it received four dead and one woman in critical condition.