The Southern Tigers' dream of becoming the first Malaysian participants in the modern iteration of the AFC Champions League was dashed after they lost 3-0 to Bangkok Glass.
After defeating India's Bengaluru 2-1 at home in the first knock-out qualifier last week, hopes were high that JDT would be able to overcome the two other opponents to qualify for the championship proper.
But Argentinian forward Luciano Figueroa's absence due to lack of fitness, on top of several more injured key players, meant that last year's MSL title-winners went into the match facing an uphill battle.
They began well with their other foreign signing, Jorge Diaz almost scoring through a freekick in the 11th minute, which was tipped over by Bangkok goalkeeper Narit Taweekul.
Despite holding their own against the Thailand side for the first 30 minutes, cracks started to show with JDT defence resorting to committing fouls to stop the home side.
Soon Bangkok drew first blood in the 28th minute through Narong Jansawek's screamer from 30 meters out, which caught JDT goalkeeper Farizal Marlias off guard before going in at the top corner.
The home side added their second seven minutes after the second half kick off, when Namibian forward Lazarus Kaimbi timed his run well to beat defender S. Kunalan and received an intelligent through pass, before slotting the ball past Farizal.
Kaimbi doubled his tally to bury JDT's hope just 10 minutes later, when he capitalised on Daudsu Jamaluddin's lackadaisical defending to sneak behind, and tap the ball into the net.
Darko Tasevski could have made it four for the homeside from the penalty spot minutes later after a foul by centreback Fadhli Shas, but his shot hit the bar instead.
JDT never looked like coming back from three goals down, and the 3-0 scoreline remained unchanged.
The defeat means that JDT will be participating in the 2015 AFC Cup instead..