AFC Cup: Take a look at this calm and composed freekick
Two goals from Nguyen Quang Hai looked to have gone to waste when Altymyrat Annadurdyyev's equaliser brought the visitors level in the second half, but substitute Van Quyet netted the winning spot-kick in the 88th minute to give the Vietnamese champions a slight edge in the two-legged tie.
Earlier, Murat Yakshiyev had silenced the local crowd with a fourth minute goal in the first half.
The two teams will now travel to Ashgabat for Tuesday's second leg, with the winners to advance to next month's Inter-Zone Play-off Final.