The loss at My Dinh Stadium in Hanoi means coach Park Hang-seo's men are still without a point after six matches in the third round of World Cup qualifying.
While the Vietnamese team put in a performance full of grit and determination, they were unable to lay a glove on the dominant Saudis, who lead Group B without a loss to their name and look set to qualify for the Qatar 2022 finals.
Coach Park named 10 of the 11 players who started against Japan on last Thursday, with only Nguyen Thanh Chung coming in for Bui Tien Dung at the back.
The first half was largely an even affair, with neither team able to carve out a clear-cut opportunity until the 30th minute, when the visitors opened the scoring.
Fahad Al-Muwallad put a cross into the box after a tricky run and Saleh Al-Shehri applied the finish with a superb, looping header that Vietnamese goalkeeper Bui Tan Truong was unable to stop creeping over the line.
The half was to end with the home side a goal down, a score line unable to silence the 9,699 spectators in attendance who were in fine voice throughout the night.
Vietnam’s first real chance to score fell to Que Ngoc Hai in the 69th minute from a set piece after Chung flicked on a delivery, but the captain was unable to direct his volley on target.
Just six minutes later, the Saudis had the ball in the back of the net again as Al-Muwallad applied a simple finish after Firas al-Buraikan squared the ball across the box after taking the ball off Chung.
However, the video assistant referee (VAR) stepped in to chalk the goal off as it did on Thursday against Japan, as the referee determined that Chung was fouled in the build-up.
The home side's best attacking spell came in the final 10 minutes as they piled forward in search of an equaliser.
Substitute Phan Van Duc had two half-chances late on as he fired wide from a tight angle in the 89th minute and then headed wide deep into stoppage time, but in truth they were both difficult opportunities.
The national team will now turn their attention to defending their AFF Championship title this winter, a competition where success is expected rather than hoped for.
On the strength of two dogged World Cup performances against much superior sides, expectations should be high.