Lawyer Clemente Heraldo, 38, chief of the Customs Investigation and Intelligence Prosecution Division, was shot in the left eye, while Mauricio Gallo, 35, a staff supervisor of Pilipinas Shell, got a bullet in the chest.
Heraldo and Gallo died at the Manila Doctors Hospital on United Nations Avenue in Ermita, Manila.
Gallos wife, Luisa, 38, who was hit by a bullet in the lower part of her body, is being treated at the same hospital.
The couples nine-year-old son Jericho, who was with them in their Toyota Revo van, escaped injury.
Witnesses said Gallo, whose vehicle was the first to be attacked by the suspects, was not the target, but Heraldo, whose blue green Pajero was trailing the Shell executive at Adonis and Leoncio streets.
Witnesses said as Gallos car emerged from Laura street, two of the gunmen, who appeared to be excited, riddled it with bullets, before finding out that they had shot at the wrong car.
"Ay mali (Wrong target)!" witnesses overheard one of the gunmen as saying.
Witnesses said at that point, Heraldo immediately backed up his car to try to escape, but the three other gunmen suddenly appeared and started firing at Heraldos car until it skidded to a halt.
After the shooting, the gunmen boarded a tricycle and got off at Carreon street, where they were seen walking toward Kahilum street near the railroad tracks, witnesses added.
Manila police investigator Senior Police Officer 1 Benito Cabatbat said the gunmen were apparently waiting in ambush for Heraldo at Adonis and Leoncio streets as early as 7:30 a.m.
Police recovered several calber .45 shells at the scene.
As witnesses gave police a sketch of one of the gunmen, they were still trying to determine the reason for the ambush.
Heraldo was the second Customs official to be ambushed in Manila.
Last July 25, lawyer Felipe Bartolome, a Customs collector at the Manila International Container Port, survived a slay try by three armed men near the Anda Circle in Port Area.
Bartolomes driver was killed in the attack.
Prior to Bartolomes ambush, the Cebu deputy collector for operations and a Customs examiner were shot dead in Cebu City.