Graham Arnold's men have failed to make the knockout stages of the AFCChampions League after they were defeated 3-0 by the 2011 J-League runners-up
The A-League outfit entered the last match of Group G in third place, knowing a win in Japan would be enough to book their spot in the Round of 16.
But first-half goals to Keiji Tamada and Jungo Fujimoto put Central Coast on the back foot, with Marcus Tanaka adding polish to the triumph with his late effort.
Graham Arnold made two enforced changes to the Mariners side that beat Tianjin Teda 5-1 in their last ACL outing, with defender Pedj Bojic [suspended] and midfielder Oliver Bozanic [injured] replaced by Trent Sainsbury and Adriano Pellegrino respectively.
Central Coast looked comfortable in the opening stages but Nagoya quickly stepped up, with Marcus Tanaka and Tamada having early chances.
And the J-League outfit soon took the lead thanks a free-kick from Tamada on 19 minutes.
The decision to award the set-piece was controversial but Adam Kwasnik gave Nagoya an even bigger helping hand when he jumped out of the wall, leaving a gap between himself and Central Coast captain Alex Wilkinson.
Tamada's left-foot effort went flying through that gap and his low effort stranded Mariners goalkeeper Mat Ryan, much to the delight of the home fans at the Nagoya Mizuho Athletic Stadium.
Central Coast's veteran defender Patrick Zwaanswijk fired a free-kick straight at Nagoya shot-stopper Seigo Narazaki shortly after and Michael McGlinchey was unable to convert the rebound.
The hosts doubled their lead 10 minutes before the break when Yoshizumi Ogawa caught the Mariners defence napping with a ball forward.
Fujimoto took full advantage as he charged towards goal before producing a delicate lob over Ryan's head and into the back of the net, as Nagoya took a two-goal lead into the break.
Central Coast had their best spell of the game in the 15 minutes after half-time, with Tom Rogic and Kwasnik causing the hosts a few problems.
Rogic had the chance to score from six yards after a neat Kwasnik ball, only for Hayuma Tanaka to take the ball from him at the last second with a superb challenge.
From the resulting corner, Rogic's curling effort was only denied by a smart Nawazaki save, while Kwasnik fired a shot over and then just failed to reach a ball that agonisingly sailed over his head right in front of goal.
Arnold attempted to change things up by introducing Bernie Ibini-Isei and Trent McLenahan just before the hour-mark, but it made little difference as the Mariners failed to keep the pressure on their opponents.
Ogawa nodded just wide on 65 minutes while Marcus Tanaka hit the side netting from an indirect free-kick and then headed straight at Ryan.
Tanaka finally got his goal with three minutes left when he powered a strong header home from close range.
And that wrapped up a convincing performance from Nagoya, who are undefeated in this year's competition.