Bikram Rai and Ajay Tamang netted for the victorious Gorkha Brigade, while Prabin Shyangtang pulled one back for the second-string APF.
Gorkha Brigade will meet Manang Marshyangdi Club in its next match.
APF coach Krishna Thapa pointed out the absence of seven key players as the reason for defeat. "Seven players including three forwards -- Bista brothers Anjan and Ranjan and Jangbu Sherpa and goalkeeper Amrit Chaudhary -- are in national duty for the Bangabandhu Cup in Dhaka," Thapa said. "However, the young and inexperienced players played well though custodian Bikram Gurung failed to justify his role."
Bikram Rai put the visitors in the driving seat as early as in the 11th minute after he pounced in a header of Chhiring Lepcha in Ajay Tamang's cross.
APF restored parity 10 minutes into second half after Pravin, the 30th minute replacement of Yubaraj Khadka, slammed in Shyam Nepali's cross from the zone.
Gorkha Brigade fought back and ensured the victory eight minutes from time after Ajay Tamang netted from the zone capitalizing on Bikram Rai's pass. Ajay was declared the man-of-the-match.
The visitors controlled the early stage of the match though the later stage was an evenly-contested affair. Not only the absence of key players but also failing to utilize some clear chances turned dear for the departmental team. APF skipper Ganesh Lawati wasted two chances in either halves including a one-on-one encounter with goalie Mani Thapa.
Gorkha Brigade coach Nargen Lama said that every team of Nepal is tough to play. "We were successful in executing our plans on the pitch," Lama said, adding that his side's next opponent MMC was also a strong side and they will plan accordingly.
According to Lama, Gorkha Brigade is an A-division team of the Indian Army and competes in All India Tournament.
Today's Match: Jawalakhel V Tribhuvan Army