The blast took place as people were leaving the Our Lady of Hope Parish. At least three people were injured in the explosion.
The Asian country raised its terror alert to "severe" after a second bomb was found outside the US embassy in Manila the following day.
The bomb was found in a rubbish bin by a street sweeper who contacted authorities before it was detonated.
Two suspected Islamist militants, Rashid Kilala and Jiaher Guinar, belonging to the militant group called Ansar Al-khilafa Philippines, were arrested on November 30.
Speaking about the increased terror alert, Fr Jerome Secillano of the bishops' conference told UCANews: "The Church, for practical purposes, will be more than willing to suspend any liturgical activity if there are threats to the safety of churchgoers."
Police said another group that has claimed allegiance to the Islamic State was believed to have been behind the foiled bombing.
Fr Secillano encouraged Catholics to remain vigilant and report any suspicious activities to authorities.