A brace from bustling Cameroon striker Jean Emmanuel Effa Owona proved enough for Negri, who had fallen behind to an early Norsharul Idlan Talaha strike in Kuala Lumpur.
Ahead of Tuesday's opening Super League games, it was Kelantan who drew first blood when last season's Most Valuable Player (MVP) Norshahrul put his team in front from close range in the 20th minute after fine work by Lebanese import Muhammed Ghaddar.
Defending Malaysia Cup champions Negri refused to buckle however, and their efforts paid dividends on the half hour mark when Effa Owona capitalised on some poor Kelantan defending to fire home a deflected shot past goalkeeper Khairul Fahmi.
Effa Owona, a major threat to the Kelantan defence throughout, bagged the winner on 63 minutes, rising high to head Tengku Qayyum Ubaidillah's cross into the net folllowing neat approach play from S.Kunalan.
"It was a memorable but difficult game as we had to come back from a goal down against a strong team. We took advantage of the opportunities that came by to win the title," Negri coach Azraai Khor Abdullah told the New Straits Times.
"It was not until Friday night that I finally decided on the line-up. We started without three regulars but their replacements did very well.
"Owona made the difference as his height and strength and ability to control and shield the ball helped us plan our game. He also combined well with Ahmad Shakir Ali."
Kelantan: Khairul Fahmi Che Mat, Azizi Matt Rose, S. Subramaniam (Nik Shahrul Azim Halim), Mohd Farisham Ismail, Mohd Aziz Ismail, Mohd Shakir Shaari, Norfarhan Mohamad, Indra Putra Mahayuddin, Norshahrul Idlan Talaha, Antwi Dennis Agyare (Mohd Badhri Mohd Radzi), Muhamad Ghaddar.
Negri Sembilan: Farizal Marlias, Tengku Qayyum Ubaidillah (Mohd Nazrin Mohd Nawi), Norhafiz Zamani Misbah, Rashid Mamud, Muzaki Abu Bakar, Abdul Halim Zainal, G. Mahathevan, Shahurain Abu Samah, S. Kunanlan, Ahmad Shakir Md Ali (Mohd Firdaus Azizul), Jean Emmanuel Effa Owona.