The pair were displaying no other symptoms but have been sent to the southern city's Tropical Diseases Hospital for isolation, the ministry said in a statement released yesterday.
Airline passengers sitting next to the pair - who travelled to Vietnam on Monday from Nigeria via Qatar - have been advised to monitor their health conditions.
Vietnam has introduced mandatory temperature checks at its two major international airports in Hanoi and Ho Chi Minh City in a bid to prevent passengers bringing the deadly virus into the country.
The global death toll from Ebola stands at 1,229, with the bulk of cases in Liberia, Guinea and Sierra Leone.
The medical charity MSF has said the outbreak is moving faster than aid organisations can handle, while the World Health Organisation said the scale of the epidemic had been vastly underestimated.