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Olivier Giroud drove home the first goal just five minutes into the game to rapturous applause from the packed stadium.
He secured a hat-trick just moments before the end of the first half.
Action gathered pace in the second half, despite hot and humid temperatures, with Arsenal scoring another four goals. As the humidity turned to rain, Vietnam fought back with a goal close to full time, but the two minutes of extra time wasn't enough to save them.
Arsene Wenger's team will wrap up their pre-season tour in Japan with two more friendlies.
They beat an Indonesian team 7-0 late Sunday.
Premiership clubs are very popular in Vietnam - much to the detriment of local teams.
Around 25 000 fans turned out to cheer Wenger and his players at My Dinh National Stadium during the training session Tuesday night.
Devoted fans have been following the North London team since they arrived in the capital on Monday.
But one fan made such a big impression that he was invited to lead Arsenal onto the pitch for the game on Wednesday, according to media reports.
The fan, dubbed "Running Man" by the club, was filmed from the window as he ran alongside the team's bus for several kilometres. He was eventually allowed onto the bus to get his shirt signed.
Despite the team's popularity, the Gunners' historic trip doesn't come without controversy.
The team's sponsor in Vietnam, business group Hoang Anh Gia Lai (HAGL), was the subject of a report in May by Global Witness, a campaign group which highlights abuses related to the exploitation of natural resources.
The group accused HAGL of acquiring vast amounts of land and contributing to environmental and human rights abuses at its rubber plantations in Laos and Cambodia.
HAGL, which is run by one of Vietnam's richest men, Doan Nguyen Duc, denied the accusations.
"As a large listed company, we always abide by the laws and regulations of countries where we do business, and we meet all the environmental criteria of Laos and Cambodia," he was quoted as saying in state-run newspaper Viet Nam News in May.
