They said the men were suspected of being members of the Abu Sayyaf group, which said it carried out the Manila bombing and two other attacks in the south of the country on the same day, killing a total of 13 people and wounding more than 100.
"Based on sketchy reports, we got a big fish," army spokesman Lieutenant-Colonel Buenaventura Pascual said, saying the two suspects were also linked to previous bomb attacks in the southern port city of Zamboanga on Mindanao island.
He said a team of soldiers and police officers arrested the two in Manila early on Tuesday, but gave no further details.
A senior military intelligence official said one of the suspects, Gamal Baharan, was involved in an October 2002 bomb attack outside an army training camp in Zamboanga City that killed an American soldier.
A police intelligence official said the other suspected Abu Sayyaf member, Amil Hajiron, was caught based on a tip from an informant who saw a sketch of the bomb suspects in newspapers and on television.
Hajiron was believed to be involved in the November 2002 bombing of a Roman Catholic shrine in Zamboanga City, the police official said.