Hong Kong forward Ho Man Chan opened the scoring in the 20th minute off an Estonian defensive mistake.
Estonian coach Arno Pijpers said the first twenty minutes of the game were quite difficult.
"That time was spent for adaptation," said Pijpers.
Estonians continued to press in the second half, and their efforts were rewarded at the 53rd minute when Indrek Zelinski scored off a pass from Martin Reimis. Zelinski score his second five minutes later. It was the second win for Pijpers in his second game as head coach. Estonia beat Kyrgyzstan 1:0 on Nov. 15.