Dempo has now moved up to 7th spot.
Khalid Jamil also created history by becoming the first Indian to coach three or more league games and guide a side to the playoffs.
Early exchanges saw both sides create half-chances. Suhair Vadakkepeedika provided Lalkhawpuimawia with a decent chance but the forward completely miscued his shot from 12 yards out, to the anger of Jamil on the sideline.
Mohamed Irshad scored a goal deep into injury time but that didn't matter in the end as Khalid Jamil's side remained on 10 points from 16 games. Kerala now have 23 points from 13 outings.
It was all Hyderabad after the first goal as they dictated the game and kept pressing the NorthEast United backline.
The win took the Highlanders to the second spot with eight points as they remained unbeaten from four matches.
NorthEast United inched closer to a playoffs berth with a 2-1 win over 10-man SC East Bengal in the ISL
NorthEast United FC were held to a thrilling 3-3 draw by Chennaiyin FC at the GMC Stadium, in Bambolim