A solitary strike from Safiq Rahim (55') was enough to see the Malaysian side secure all three points.
The game got off to a fairly even start as both sides looked to build momentum.
The first shot on target came from the visitors as Diaz's effort was comfortably collected by Ralte in the 16th minute.
The Bengaluru custodian was handed a much sterner test for his second save of the game though. Lucero's shot looked destined for the far corner but Ralte did well to dive to his right and get a hand to the ball in the 22nd minute.
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Diza then spurned a great opportunity in the 41st minute. Ralte intercepted a cross but the loose ball fell kindly to the striker who could only shoot wide.
The hosts finally got a shot away at goal two minutes later. At the end of a neat counter-attack, Thoi Singh pulled the trigger but his shot was straight at Izham who made a routine save as the teams went into the break with the tie level at 0-0.
However, when JDT won a free-kick of their own, they made it count. Safiq Rahim's direct effort went straight into the back of the net to give the away side the lead in the 55th minute.
Chhuantea Fanai tried his luck from range in the 76th minute as Bengaluru grew desperate in their search for an equaliser but his shot was off target.
Keegan Pereira was the next in line to have a go at the end of a good attack by the Blues but once again, the final shot went wide.
Despite Bengaluru's best efforts in the closing stages, the away team held on for a slender 1-0 win which took them to the top of Group H with six points in two games.
Ashley Westwood's side, on the other hand, remain bottom having failed to register a point in the opening two fixtures.