This was the play-off's first round match and last season's I-League winners will get two more opportunities.
The best chance of an evenly fought first half fell to the visitors when Englishman John Johnson - named the I-League's best defender in Bengaluru's championship winning season - headed in Beikhokhei Beingaichho's 23rd minute corner.
When the deadlock at the Stadium Tan Sri Dato' Haji Yunos was broken two minutes after the interval it was via a move that was almost identical to the Bengaluru miss when Singapore international Hariss Harun, who was admittedly afforded more space than the former Middleborough defender, connected with Nazrin Nawi's corner and unleashed a header past Ralte Lalthuammawia and into the back of the Bengaluru net.
But the equaliser did come from the resulting corner with Lyngdoh's superbly-struck set-piece swerving at speed towards the far post which Rahim could only fire into the roof of the net as the JDT skipper attempted to volley clear the delivery.
Jorge Pereyra Diaz, who saw his stoppage-time free-kick comfortably gathered by Bengaluru keeper Lalthuammawia with what was the last kick of the regulation 90 minutes, unlocked the visitors' defence with an intelligent pass into the penalty area allowing fellow substitute Suppiah Chanturu to side-foot JDT into a 2-1 lead, six minutes into extra time.
Lalthuammawia almost gifted JDT at the death when he scuffed a weak clearance directly to the feet of Chanturu, but the 27-year-old's weak effort was comfortably gathered by the grateful keeper.
The miss didn't prove too costly, however, with Bengaluru unable to find a last-gasp equaliser for the second time in the match as the Southern Tigers move on to the next phase in their campaign to qualify for Asia's premier club competition.
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