The defeat means coach Park hang-seo's men are still without a point in the third round of 2022 World Cup qualifying after three matches.
The first half ended with no goals scored although both sides had chances.
Players of Vietnam (in white) and China vie for the ball. (Photo: AFC)
Chinese striker Zhang Yuning tested Vietnamese keeper Bui Tan Truong just two minutes into the match but his right-footed shot from the left side of the six-yard box missed to the right.
Star Chinese forward Wu Lei had two consecutive chances to score minutes later but both of the Espanyol man's attempts were denied.
The visiting side also had six attempts with three from striker Nguyen Tien Linh, who scored a double in a friendly match which saw Vietnam’s U22 team beat China’s U22 squad 2-0 in 2019.
Just seven minutes after the break, Zhang opened the scoring after Truong parried Wu’s close-range shot into his path.
The goal spurred China on and they doubled their lead in the 75th minute, with Wu's movement in the box superb to find room for a headed finish.
However, the Vietnamese side refused to lie down and substitute Ho Tan Tai pulled a goal back in the 80th minute.
Tai was played in thanks to a long pass from midfielder Nguyen Hoang Duc which beat the entire China defence. Tai controlled it with his right foot and fired it home with the left.
In the final minute of normal time, Linh got his reward for a night of hard graft by converting a smart pass from midfielder Nguyen Quang Hai to level the scores.
With five minutes added on it seemed either team could have taken all three points, but it was to be the nominal home side that triumphed.
Wu found room in the box after more brilliant movement in the 95th minute and glanced home a deep cross, condemning Vietnam to defeat.
"Scoring in the last minute makes me happy but it is pity that we could not hold the draw result to the end. If we had been lucky we may have got a win, but this is football," said Linh.
Vietnam will next play Oman on October 12 while China will take on Saudi Arabia a day later./.