The home team drew first blood when Redeem Tlang scored the quickest goal of the season in the second minute. Odisha equalised through Xisco Hernandez (71') before defender Carlos Delgado was sent off.
The Highlanders made their advantage count through Gyan who popped up with a header six minutes from the final whistle.
The win takes NorthEast to the top of the table while Odisha slumped to their second loss in as many matches.
The hosts enjoyed the best possible start to the game when they roared into the lead with just two minutes on the clock. Martin Chaves started the move with a run down the left flank before finding Panagiotis Triadis down the middle. The Greek midfielder found Tlang in space down the right and the youngster tucked a finish past Arshdeep Singh to send the home crowd into raptures.
Odisha head coach Josep Gombau made a double change at half-time, bringing in Senegalese midfielder Diawandou Diagne and winger Nandhakumar Sekar. And the substitutes almost immediately did the job for Gombau.
Diagne, after a good run down the right, flashed a dangerous cross across the face of goal in the 51st minute. Nandha went close for Odisha soon after as Odisha turned up the heat on NorthEast.
The pressure finally paid off in the 71st minute when Diagne's brilliant cross from the right was flicked in smartly by Xisco with the outside of his left boot.
However, drama ensued two minutes later as Delgado was sent off for bringing down NorthEast substitute Maximilian Barreira. With numerical advantage on their side, NorthEast piled on the pressure.
They created a flurry of chances before finally getting the winner six minutes from time. Lalthathanga Khawlhring's corner was headed in by star striker Gyan to hand his side their first win of the season.
( With inputs from IANS )