The carrier, which operates 11 direct air routes between Vietnam and South Korea, or 480 flights a month, confirmed its decision as over 5,300 infections and 32 deaths have been reported in the country.
However, Vietjet Air will help repatriate South Koreans stranded in Vietnam to Incheon Airport in Seoul before the suspension takes effect.
National flag carrier Vietnam Airlines stopped flying to South Korea from Wednesday while private carrier Bamboo Airways halted services to the country on February 26.
Around 200,000 Vietnamese citizens study or work in South Korea, 8,285 living in Daegu and 18,502 in North Gyeongsang.
The country suspended its visa waiver for South Koreans starting last Saturday.
Vietnam has recorded a total of 16 Covid-19 patients, all of whom have recovered and been discharged from hospital. The country has reported no new infections since February 13.