Military spokesman Ramon Zagala said agents arrested Jovito Palparan in Manila.
Justice Secretary Leila de Lima said the arrest of Palparan showed the government would "end the culture of impunity" characterised by human rights violations under Aquino's predecessor, Gloria Arroyo.
Palparan, 63, has been on the run since December 2011 after a court issued a warrant for his arrest over the kidnapping and disappearance of two female left-wing activists in Bulacan province north of Manila in 2006.
The two remain missing. The retired major general, who was in charge of a regional army unit, has denied any involvement.
Human rights groups and a UN investigator have blamed security forces for the deaths and disappearances of about 1,000 activists between 2001 and 2010 under Arroyo. The former president gave the military a free hand in what it called an all-out war against communist rebels.
Aquino's government has said it wanted justice for the missing students, Karen Empeno and Sherlyn Cadapan, to improve the Philippines' human rights record after a decade of abuses under the previous administration.
"The human-rights community, domestic and international community, has long waited for this," de Lima said.
She said an arraignment date would be set by Bulacan's provincial court.
A breakthrough in the case came late on Monday when naval intelligence agents checked a tip from an informant and spotted Palparan in the crowded suburban Manila neighbourhood, said military intelligence service chief Major General Eduardo Ano, who has headed a task force assigned to capture the fugitive general.
In 2012, Aquino doubled the reward for the capture of Palparan, along with a former governor wanted in the killing of an environmentalist and a former congressman convicted of murdering his wife, to 2 million pesos, with officials saying the president was unhappy at the lack of progress in arresting high-profile fugitives.