Coach Dinh The Nam's team of youngsters dominated the match and found goals through Ha Chau Phi and Nguyen Duc Viet, as well as a brace from Nguyen Gian Tan.
Vietnam were down to 10 men in the last 10 minutes of the match, after keeper Ho Tung Han handled outside the box, but stayed strong and kept a clean sheet.
Facing a dismal Brunei that has conceded 14 goals in their last two matches against Indonesia and Myanmar, Nam chose to rest key players Khuat Van Khang and Nguyen Van Truong and grant chances to reserves such as Tung Han and Gian Tan.
It took only 12 minutes for Vietnam to open the scoreline when Thai Van Thao's corner found Chau Phi at the far post. The right-back, whose name translates into English as "Africa", easily overpowered his opponent to tap in his first-ever goal for Vietnam U19s.
The Vietnamese then seemed to lose concentration and gave the ball away easily to the Bruneians, with Hoang Anh Gia Lai's Nguyen Duc Viet mostly at fault.
Brunei couldn't seem to capitalise and conceded a second goal in the 33rd minute when Van Thao again crossed for Gian Tan, who got the ball over the line and doubled Vietnam's lead.
Vietnam started the second half slowly in the first 10 minutes to conserve energy before increasing the pace from the 55th minute.
Văn Thao, with a man of the match performance, gave his third assist of the match and granted Gian Tan his brace in the 59th minute.
Only four minutes later, Duc Viet silenced his critics with a wonderful long-range strike into the top corner after the ball rebounded off the Bruneian defence.
Suffering from fatigue, Brunei gave up, and multiple chances came to the men in red. A consolation goal for them seemed unimaginable, given the total pressure and possession that Vietnam had.
That is until Vietnam's keeper Tung Han handled the ball outside the box after a poor backpass from his teammate. The young keeper protested, but the referee was decisive and brandished Han with a straight red.
Brunei pushed forward and made Vietnam's 10 men work hard in the match's final minutes. Vietnam also got chances on the counter, but no more goals were scored.
With this result, Vietnam temporarily took the lead in Group A with 7 points before Thailand and hosts Indonesia face off later on Wednesday. Brunei are eliminated and share the same fate as the Philippines who lost 3-1 to Myanmar earlier.
Having only scored four against the bottom team, Coach Nam is at a disadvantage should it come to tiebreakers against the remaining teams in Group A.
Vietnam have two days to rest before facing Myanmar in Jakarta July 8, and a win will secure their place in the semifinals.