Having suffered a heavy 4-0 away loss in the first leg of Round 1 last Thursday, Bhutan took the lead just before the half hour of the return meeting at Changlimithang Stadium through captain Chencho Gyeltshen before Lobzang Chogyal made it two early in the second half.
But a third goal was not forthcoming as Hong Kong held out to progress to Round 2, where they will join Islamic Republic of Iran, Uzbekistan and Turkmenistan in a tricky looking Group E.