The MNLF was formed to seek autonomy for the Philippines' Muslim-majority Moro state in a country that is predominantly Christian.
Dolorfino and Santos had flown in on Friday morning for talks with the MNLF about a shaky 1996 peace agreement and clashes between government troops and its members.
Habier Malik, a rebel commander, had refused to let them leave until he received assurances that a meeting about the 1996 deal would take place in Saudi Arabia between the government, the MNLF and the Muslim world's largest grouping, the Organisation of the Islamic Conference (OIC).
Malik also wanted the general to apologise for the killing of nine MNLF members and civilians in an encounter with marines last month.
Three soldiers were also killed in the clash on the island of Jolo.
The MNLF has said that the military wrongly identified the dead as members of Abu Sayyaf, a group of militant Islamist separatists who broke away from the MNLF, which Manila has vowed to crush.
In a ceremony filmed by local television, Malik handed over four assault rifles seized by the MNLF in the fatal encounter.
"We just co-operated with them. No cash paid, only sacks of rice and some sardines for the families of the victims of [the] January 18 encounter," Dolorfino said.