Bhutan played their first qualifier against Sri Lanka last week in Colombo and returned home with a 1-0 lead thanks to Tshering Dorji's late goal.
And a 2-1 win in Thimphu's Changlimithang National Stadium ensured progression to the second qualifying stage, where they will be grouped among the continent's big hitters.
Coach Chokey Nima saw Gyeltshen score either side of Zohar Zarwan's leveller to ensure a historic win, with Timor-Leste also moving to the second round of qualifying for the first time while India knocked out Nepal.
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