The flights will depart from the central city of Da Nang at 2:55 a.m. and arrive in Narita at 1:20 p.m. (local time).
The national flag carrier will maintain the route until March 31 next year. After that date, it will fly between Da Nang and Narita directly without transiting Ho Chi Minh City(HCMC).
The national carrier will also open a direct route between Da Nang and Hong Kong on November 26, according to the Da Nang People’s Committee.
On Monday, it launched a second direct route to Yangon, Myanmar's southern trade hub and former capital city.
There will be three flights a week between Yangon and HCMC, the airline said.
The carrier had begun flying from Hanoi to Yangon four times a week in March.
A member of the SkyTeam airline alliance that includes Air France and America's Delta Airlines, Vietnam Airlines has set out to become one of Southeast Asia's leading carriers.
It aims to transport 12 million passengers this year and boost its fleet from 70 to 115 aircraft by 2015.