Ngoubo Singh put Manipur ahead in the 27 minute when he found the net from a free kick. In the 52nd minute, Manipur captain Nilakumar scored the second goal for the winners.
The result was disappointing for the home crowd, who had gathered at the Dimapur District Sports Council (DDSC) stadium.
Manipur earned Rs seven lakh as prize money while the runners-up got Rs four lakh. The tournament witnessed participation from all the eight NE states.
Tripura, riding on Kiron Chattri's hat-trick had clinched the third place after defeating Meghalaya 3-0 on Wednesday.
Kiron was also the top scorer of the tournament with 14 goals while Manipur striker Malemnganba Metei scored eight and Nagaland's Sakutemjen scored seven goals.
The tournament was named after legendary Naga footballer Dr Talimeren Ao.
Nagaland governor Nikhil Kumar and chief minister Neiphiu Rio and Meghalaya deputy chief minister BM Lanong gave away prizes to the winning teams and individual players.
Dr Ao, who led the independent India's football squad in 1948 London Olympics, played for Mohan Bagun from 1942 to 1949 while studying at Kar Medical College, Kolkata.
The barefoot Olympian who captained the Bagan XI during 1947-49, was first Naga MBBS and retired as the state director of health and medical services.