Kamaljit Singh's poor clearance found Ralte whose pass went straight into the path of Chhetri who made no mistake in slotting the ball home.
At the stroke of half-time, Odisha had a great chance when Santana slipped Jerry in behind the defence, but his shot went wide of the far post.
At the other end, Gyan's firm shot from a quick break was well saved by the Mumbai goalkeeper, keeping the scoreline intact.
Goa were reduced to 10 men towards the end of the second half when Ahmed Jahouh, who had picked up a yellow card in the fifth minute.
Hyderabad FC defense was caught off guard at times but skipper Kamaljit Singh led from the front and came up with a few good saves.
After a 13-day break, two southern rivals — Bengaluru FC and Kerala Blasters — will resume the Indian Super League action at the Sree Kanteerava Stadium on Saturday.
Sergio Castel reduced the margin for Jamshedpur FC in the 85th minute with yet another penalty after Anas Edathodika brought down Noe Acosta in an ugly challenge inside the box.
Kerala, who were already hampered by injuries this season, suffered a major blow in the fourth minute when captain Rodriguez went down injured.
Mumbai refused to sit back and let Goa pass the ball around in the opening minutes but the hosts, however, failed to test Mohammed Nawaz's goal during that period.
Memories from last season, where Kerala went on a 14-game winless run after their win over ATK in the opening match is still fresh in the minds.
FC Goa has also been served with a similar show cause notice for failing to control its substitute players and officials from entering the Field of Play without permission and participating in the inc
The teams had their fair share of moments in a closely-contested tie, but a spot-kick off a handball in the 86th minute helped NorthEast United edge past their opponents.
As per the schedule, the Odisha FC is to face ATK, Bengaluru FC and Hyderabad on November 24, December 4 and December 11 respectively at Kalinga Stadium here.
The result takes Jamshedpur to the top of the table with seven points from three outings.
The 2-1 win was made possible by a penalty from Marko Stankovic and a superb free-kick from Marcelinho.