Nagoya drew first blood as early as in the fourth minute after JDT's Adam Nor Azlin fouled striker Matheus in the penalty box. The Brazilian duly delivered by scoring the penalty past goalkeeper Haziq Nadzli.
The Japanese club added a second in the 29th minute when winger Hiroyuki Abe curled in a beautiful left-footed shot from outside the penalty box.
The Southern Tigers reduced the deficit in the 42nd minute through winger Ramadhan Saifullah who tapped a rebound from Nagoya’s goalkeeper Mitchell Langerak off a shot by Leandro Velasquez.
JDT knew earlier that they would not qualify for the knockout stages after Pohang Steelers were held 0-0 by Ratchaburi FC in the earlier group game.
Nagoya and Pohang will move to the next stage as they have 15 and 10 points respectively while JDT remained third with three points. JDT will complete the fixture when they take on Ratchaburi FC on Tuesday (July 7).