Sabban said he ordered a "surgical assault" on the camp after intelligence reports indicated an "unusual convergence" of leaders of the Abu Sayyaf group.
These were believed to include one of their most wanted commanders, Radulan Sahiron, as well as Umar Patek, a member of the Indonesia-based group Jemaah Islamiyah.
Key members of Jemaah Islamiyah are believed to have fled to Jolo island in 2003 and taken refuge with the Abu Sayyaf.
The military commander said artillery fire on the base destroyed a facility for assembling bombs, similar to those used in attacks in nearby Zamboanga city and other areas.
Marga Ortigas, Al Jazeera's correspondent in the Philippines, said that despite the apparent success of the operation the military was troubled by the presence of fighters from the Moro National Liberation Front in the battle.
The MNLF signed a peace accord with the Philippine government in 1996 in exchange for the establishment of a Muslim autonomous area.
It had previously launched a bloody separatist war in the southern Philippines in the 1970s.
Although the Abu Sayyaf is estimated to have 380 men, down from 1,000 in early 2000, it is still considered by the government to be dangerous terrorist group.
The group is believed to have launched its last major attack in February 2005 with simultaneous bombings in Manila and two southern cities that killed eight people and wounded more than 100.
While mainstream Muslim rebel groups in the Philippines have signed truces with Manila and are negotiating for some measure of self-rule in the south, the Abu Sayyaf continues to bomb civilian targets and uses kidnap-for-ransom to fund its activities.