With the triumph, Vietnam further tighten their grip on the top of the group with 14 points.
Nguyen Tien Linh opened the scoreboard for the team in six minutes into the second half, before Nguyen Quang Hai, substitute Nguyen Cong Phuong and Vu Van Thanh extended the lead.
In their previous face-off in the qualifiers in October 2019, Vietnam defeated their Indonesian rivals 3-1.
State President Nguyen Xuan Phuc and National Assembly Chairman Vuong Dinh Hue congratulated the squad on its victory, according to the Vietnam Football Federation (VFF).
The team also received a bonus of VND 1 billion (USD 43,590) from the VFF.
Vietnam will play Malaysia on June 11 and UAE four days after then.