Ganesh Khadka scored the winner slotting home in the 81st minute amid the raucous home support.
"Ganesh has a knack for taking the right decision at the right time. His very gift won us today's match," said Jhapa's coach Bhagirath Ale after the match.
The important win gave Jhapa two-point advantage over Manang with 13 points from six matches. This is the first win for Jhapa at home.
African-recruit Ahmed Abbas had a major role in Jhapa's win as he was the one who created the opportunity for an all-important goal.
Nevertheless, his initial two attempts at goal failed to find the back of net before Ganesh's goal, which he scored capitalizing on the second rebound off the African-recruit's attempt at goal.
Abbas's first shot was parried-away by Manang's goalie Bishal Shrestha while his second attempt was blocked by a defender, which fell into Ganesh's way.
Both teams had come into the match with their eyes set on the top of the table.
Abbas substituted Jhapa's regular striker Bishal Rai in the 80th minute. The decision became fruitful for Jhapa.
The match attainted aggressively attacking tone right from the onset. Manang started with Anil Gurung, Shiva Shrestha, Sujal Shrestha and Leonce Dodoz to resort into attacking mindset.
"Anil was not in his best shape today and our shooting was sloppy. Our defense lost its coordination in last 20 minutes. That was the reason for today's loss. The loss stunned us," said Manang coach Raju Shakya.
Far West and Army share spoils
DHANGADI: Tribhuvan Army Club missed out on its opportunity to cut its gap by one point against leader Jhapa XI in the Red Bull National League after it was held 1-1 by Far Western FC at the latter's home in Dhangadi on Sunday.
The draw leaves Army in the fourth place with 10 points, three points behind Jhapa and one point less than second and third placed Manang Marshyangdi and Nepal Armed Police Force respectively, who are level on 11 points.
Meanwhile, Far Western stands seventh on the table with six points as Nepal Police Club.
Tek Bahadur Budathoki put Army early on the lead breaking the deadlock five minutes into the match.
Man-of-the-match Label Dalekan Afeez leveled the score in the 37th minute.
APF steals narrow win over Lumbini
BUTWAL: Nepal Armed Police Force (APF) climbed third in the standings after sneaking a narrow 3-2 win over home team Lumbini FC in Butwal on Sunday.
The win helped APF shortening its gap with leader Jhapa down to two points. It is leveled on points with second-placed Manang Marshyangdi Club on 11 points and enjoys one point cushion over fourth Tribhuvan Army Club.
The defeat kept Lumbini rooted at second form the last at eighth with four points. It trails Far Western by two points and enjoys one point advantage over bottom-placed Morang FC.
Heman Gurung put APF on front only two minutes into the match, before Nabin Lama had doubled its advantage in the ninth minute. Ganesh Lawati made it 3-0 scoring in the 19th minute.
Lumbini pulled a goal back through Pukar Gahatraj in the 54th minute while Manoj Gurung cut the deficit to one scoring in the 64th minute.
Manang lifts Jhapa Gold Cup