"I believe this will wind down within the day," he said before boarding a jet that flew him out of Zamboanga, where thousands of elite troops have been fighting Moro National Liberation Front(MNLF) gunmen for two weeks.
Aquino also vowed to bring criminal charges against MNLF founder
Nur Misuari, accused of being behind the rebel incursion.
About 200 MNLF rebels entered Zamboanga, a major trading centre with one million residents, on September 9 in the most serious armed challenge to the Philippine government in recent years.
They took over several coastal districts, burning thousands of homes and taking scores of civilians hostage, in protest at an impending peace deal with a rival Muslim rebel group.
Aquino flew to the area on September 13 to take direct command of operations, vowing not to leave until the gunmen are pushed back out of the city.
Military spokesman Lieutenant-Colonel Ramon Zagala said the armed forces backed their commander-in-chief Aquino's latest pronouncement.
"The armed forces support the president's statement that this is almost over," Zagala told AFP.
"We will work hard to finish this soonest."
He said about 4,500 soldiers remained in the city to clear it of guerrillas after two weeks of deadly street battles that left hundreds dead or injured.
More than 10,000 houses were set on fire and 111,000 civilian residents fled the street battles, according to the civil defence office in Manila.
The military said there are now just several dozen fighters left, holding at least 20 hostages in one neighbourhood of dense clusters of homes.
"We're now engaged in close-quarter combat, we are going from house to house, room to room," Zagala told AFP earlier Sunday.
One soldier was killed and 10 others were wounded in the past 24 hours, Zagala said.
In two weeks of fighting 102 guerrillas have been killed with 117 others taken into custody, he said.
Fourteen soldiers and police died and 114 were wounded, he added.
Twelve civilians were killed and 49 wounded, while more than 170 hostages have been freed or were able to escape, Zagala said.
Aquino, speaking to reporters at a Zamboanga air base, said state prosecutors are gathering evidence ahead of filing criminal charges against Misuari, whom the government accuses of being behind the Zamboanga attack.
"We now have witnesses who will directly link him to this conflict, and the charges are being prepared by the Department of Justice," he added.
Government officials earlier accused the Zamboanga gunmen of committing rebellion, arson, murder and hostage-taking.
Muslim rebels have been fighting since the 1970s for an independent or autonomous homeland in the south of the mainly Catholic Philippines. An estimated 150,000 people have died in the conflict.
The MNLF signed a peace treaty in 1996 that granted limited self-rule to the south's Muslim minority.
However MNLF founder Misuari deployed some of his men to Zamboanga to demonstrate opposition to a planned peace deal between the government and the remaining major Muslim rebel group, the 12,000-strong Moro Islamic Liberation Front.
The MILF is close to signing the peace pact, which Misuari believes would sideline the MNLF.
