The loss saw Binh Duong lose their top position in the rankings to Thanh Hoa, who defeated Can Tho 2-0.
Pape Omar Faye scored a goal in the 42nd minute, and Duc Tuan scored again four minutes later.
Binh Duong are now placed second in the rankings with 32 points, two less than Thanh Hoa, who achieved their fourth win in a row.
Yesterday's victory helped Khanh Hoa improve their position in the rankings. They are now ranked seventh with 24 points and will meet Quang Nam in the next round.
Quang Nam yesterday scored a 4-0 win over Hoang Anh Gia Lai on their home turf. Their biggest victory ever in V.League 1 lifted them in the rankings while pushing the visitors deeper into crisis.
Coach Guillaume Graechen said at the post-match briefing that Hoang Anh Gia Lai were "paralytic" after their 11th winless match.
The former champions, who had started the season with a promise to spring a surprise, have almost hit rock bottom when it comes to rankings, though all their players were trained methodically by international trainers employing advanced techniques.
Graechen said his lack of experience in his first V.League 1 year was part of the reason his team had played below expectations. He said his players were very young and needed time to sharpen their skills in the tough competition.
The Frenchman said Hoang Anh Gia Lai would improve soon once their injured players are back in action in the next few weeks.
Hoang Anh Gia Lai have 10 points, the same as bottom-placed Dong Nai, who managed a surprise 1-1 draw against Song Lam Nghe An after conceding a goal in the 13th minute.
Ha Noi T&T scored a big win yesterday, trouncing Dong Thap 7-0 with the help of a hat-trick by Nguyen Van Quyet and a double by Gonzalo after Hoang Vu Samson's opener. The remaining goal was an own goal by defender Quoc Anh.
At the Lach Tray Stadium, hosts Hai Phong were held to a 1-1 draw by Dong Tam Long An.
In another match, Quang Ninh Coal defeated former champions SHB Da Nang 1-0.
