Two dead bodies were taken to the Jolo provincial hospital, an official there confirmed, while Navy spokesman Lieutenant Colonel Edgard Arevalo said the number of wounded stood at 24.
Witnesses said at least seven people had suffered shrapnel injuries.
"Many of the wounded are in critical condition so there is a possibility that there will be more than two deaths," Arevalo told reporters on Tuesday. "We are still investigating who carried out the bombing," he said.
Police said another bomb was found near the Mount Carmel Catholic cathedral, also in Jolo, and disarmed.
No one claimed responsibility for the attack, which came just two days after a bomb blamed on Islamic separatist rebels exploded outside a Catholic church in Cotabato city, also in the south, killing five and wounding about 50 others.
Abu Sayyaf Muslim militants are known to operate on Jolo, where the Al Qaeda-linked group has been holding hostage an Italian Red Cross worker since January.
In May, the island province's governor Abdusakur Tan escaped a roadside bomb attack by the Abu Sayyaf that wounded five of his bodyguards.
The Abu Sayyaf has been on the run from a military offensive launched after they kidnapped Italian aid worker Eugenio Vagni in January. A Filipina and a Swiss colleague abducted with Vagni were separately freed in April.