Sasmita Malik (68th) and Ratanbala Devi (70th) scored as India ended their campaign with this lone win and finished the five-team Group B at fourth position with three points.
India had already crashed out of the tournament after suffering heavy defeats at the hands of North Korea, South Korea and Uzbekistan.
India largely dominated the match at the Kim II Sung Stadium but they could not break down the Hong Kong defence often. But they were able to pump in two goals in the later part of the second half to end their campaign on a high.
Hong Kong could have taken the lead seven minutes later after Yiu Hei Man threaded a perfectly timed pass to release Ng Wing Kum only for the midfielder to blast her shot over the bar.
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Ratanbala and Bala Devi formed a lively partnership, combining effectively to create another decent chance from the left, before the former squandered India's one more opportunity with 30 minutes played.
India began the second half with more intent and with coach Sajid Yousof Dar urging his side to increase the tempo, the South Asians turned to substitute Malik Sasmita who came close to breaking the deadlock with a fine effort in the 59th minute.
India finally went ahead when they were awarded a penalty on the 68th minute following Ip Yuen Tung's foul on Ratanbala Devi. Sasmita duly stepped up to send Leung the wrong way and netted India's second goal of the qualifiers.
India coach Sajid Dar said his wards displayed their capabilities against a good team.
"The girls showed they can play good football and when it comes to teams that are on par with us, we are indeed a better side. I would like to thank DPR Korea for hosting us. It has a great learning experience and we really enjoyed playing here," he said.
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