President Rodrigo Duterte told reporters in Manila that there "there is no doubt" about the fact that Abu Sayyaf, an armed group that has sworn loyalty to the Islamic State, was behind the explosions.
The woman left a bomb inside the Cathedral of Our Lady of Mount Carmel on the island of Jolo and fled before her husband blew himself up outside.
112 people are injured when the bombs exploded during the Mass service.
Jolo Island has long been troubled by the presence of Abu Sayyaf militants, who are blacklisted by the US and the Philippines as a terrorist organisation because of years of bombings, kidnappings and beheadings.
The attack was carried out just days after minority Muslims in the predominantly Roman Catholic nation approved expanding Muslim self-rule in the southern Philippines.
It was hoped the move would end nearly five decades of a separatist rebellion that has left 150,000 people dead.
While most of the Muslim areas approved the autonomy deal, voters in Sulu province, where Jolo is located, rejected it.
Delfin Lorenzana, secretary of the Defense of Manila, told reporters that the president has ordered the military and police to put a stop to the militants of Abu Sayyaf "by any means".
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