Major Gamal Hayudini, an army spokesman, said no group had declared responsibility for the attack, but local police suspected that the armed separatist group Abu Sayyaf was behind it.
"We're still investigating to determine the type of bomb," Hayudini said.
The explosive device was planted on the ground floor of a two-story building along a busy street in central Jolo.
Last month, a crude bomb ripped through a row of night clubs outside an army base on Jolo, killing a man and wounding 13 people, days before 250 US troops were due to conduct humanitarian missions on the island.
Jolo is the stronghold of Abu Sayyaf, a small but deadly Muslim rebel group that has been blamed for the bombing of a ferry in February 2004 that killed more than 100 people.
Abu Sayyaf is believed to have links to al-Qaida and Jemaah Islamiah, the Southeast Asian Islamist extremist network.
The group has also kidnapped and beheaded foreign and Filipino tourists and church workers.