The result also meant Khalid Jamil is still unbeaten in the competition and extended NorthEast's winning run to ten games.
Goa were keen to impose themselves on the Highlanders and came close in the fifth minute. Fernandes played a long diagonal pass from inside his own half to find Mendoza on the flank, but the latter shot straight at keeper Subhasish Chowdhury.
Hyderabad settled the tie in their favour in the second half through late goals from substitute Liston Colaco (85', 90').
With one point from the match, the Highlanders are placed joint second with ATK Mohun Bagan on 10 points
NorthEast United FC were held to a thrilling 3-3 draw by Chennaiyin FC at the GMC Stadium, in Bambolim
The 2021 men's and women's U-17 European Championships have been cancelled due to the impact of the COVID-19 pandemic, UEFA said on Friday.
Barcelona must to wait to confirm a place in the Champions League last 16 after dropping points for the first time in Group D in an absorbing 0-0 draw at Olympiakos Piraeus on Tuesday.