All four goals were scored in the second half by Nguyen Tien Linh, Nguyen Quang Hai, Nguyen Cong Phuong, and Vu Van Thanh.
Vietnam had many chances in the first half, having a total of eight corners against Indonesia's none, but failed to turn them into goals.
With Monday's victory, Vietnam now have 14 points and remain the best team of group G in the World Cup Asian qualifiers.
They have two more games in the second round against Malaysia on June 11 and UAE on June 15, from which they will need seven points to advance to the third and final round of the qualifiers.
Key midfielder Nguyen Quang Hai received a yellow card and will be absent in the next game, which coach Park Hang-seo said will be a disadvantange to Vietnam's strategy.
"But we have prepared different scenarios," he said. "We have prepared two scenarios for each position and we can make changes when needed."