They would resume when the epidemic is better controlled, the state-owned carrier said in a statement.
Its five flights between the two countries on Tuesday and Wednesday will land in Quang Ninh Province and Can Tho City since flights from that country have already been prohibited in Hanoi and Ho Chi Minh City.
The flight crews will wear protective garb, and all aircraft returning from South Korea will be disinfected.
Private carrier Bamboo Airways halted services to South Korea on February 26.
But budget carrier Vietjet continues to fly to South Korea, where there have been over 4,800 cases of coronavirus infection so far and 28 deaths.
Authorities have ordered people arriving from South Korea to be quarantined for 14 days.
Vietnam has had 16 confirmed cases, but all the patients have recovered, and there have been no new cases since February 13.