Government troops also captured 45 rebels and rescued six hostages in the village of Sta. Catalina near Zamboanga City, the Philippine Star reported.
The military said 69-year-old Misba Baladji, a female MNLF commander, led the group of rebels in surrendering.
Another 38 rebels were captured earlier in the day.
In another clash, three MNLF rebels were killed and five soldiers wounded in what security authorities said was a mopping up operation in the area.
Government forces now have 24 fatalities and 185 wounded since fighting broke out in Zamboanga City Sept. 9. At least 12 civilians have been killed and 72 wounded.
Troops also have rescued 184 civilians from MNLF rebel groups who used them as human shields, the Philippine Star reported.
The military estimates MNLF dead at 138 with 215 captured or surrendered. However, retreating MNLF sometimes hastily bury their dead, making accurate estimates of their dead difficult.
Zamboanga, at the southern tip of Mindanao Island, is one of the country's most restive regions where Muslim groups have been fighting for autonomy and independence from the federal government in Manila for decades.
The latest fighting broke out when around 200 followers of MNLF faction leader Nur Misuari stormed Zamboanga City in boats with a plan to raise the flag of the "independent Bangsamoro Republic" at city hall.
But government troops pushed the rebels back into seaside villages where fighting continues, The Inquirer reported.
Military spokesman Lt. Col. Ramon Zagala said an air assault Thursday helped troops overrun Camp Sumatra, a suspected MNLF base on an islet off the Zamboanga Peninsula.
He said the camp was a potential launching base for another attack on Zamboanga City.
"The troops captured the area following the intense ground and air support for two days," Zagala said.
"The [military] operations have prevented rebels from reaching the other MNLF group on the mainland."
The government-run Philippines News Agency said the military believes another MNLF commander, Habier Malik, remains trapped within the military "area of operations" in Zamboanga City where house-to-house fighting continues.
Zagala said the government "continually assesses" information on how many hostages are with the MNLF.
The military also said it will reopen part of the passenger ferry port facilities in Zamboanga City today [Friday] which has been closed since fighting began in earnest Sept. 9.
Zamboanga Coast Guard Station Commander Lt. Joemark Angue said there will be four trips daily between Zamboanga City and the Basilan, Sulu and Tawi-Tawi areas.
But the military will monitor passenger identity papers and inspect ships.
"No vessel can sail directly into Zamboanga City without being inspected," he said.
The MNLF wasn't part of last year's peace talks where the Moro Islamic Liberation Front and the government agreed to set up a new semi-autonomous area in the region.
But fighting has stalled implementation of the agreement.
The area is to be about the same as the existing Autonomous Region in Muslim Mindanao, which President Benigno Aquino said, after announcing the agreement, was a "failed experiment."
An elected government to administer the new region -- whose "Basic Law" will be based on Islamic Sharia law -- should be in place sometime in 2016, the detailed framework agreement available on the presidential website stated at the time.