They are both now self-isolating, said the ministry. It is unclear whether the cases are linked to South Africa.
It comes just hours after the UK announced that the first two cases of the Omicron variant had been detected in Essex and Nottinghamshire.
The new B.1.1.529 variant, first detected in Botswana, has sparked alarm among scientists due to its high number of mutations. Senior scientists have said it is the worst strain they have seen so far during the pandemic.
The variant was first discovered in South Africa and had also since been detected in Belgium, Botswana, Israel and Hong Kong. A string of countries have suspended air travel from southern Africa in a bid to halt its spread.
Although epidemiologists say travel curbs may be too late to stop Omicron from circulating globally, many countries around the world - including the United States, Brazil, Canada and European Union nations - announced travel bans or restrictions on southern Africa on Friday.
Britain also said it was expanding its “red list” to put travel curbs on more southern Africa countries, while South Korea, Sri Lanka, Thailand, Oman and Hungary also announced travel restrictions on southern African nations.
Germany is already battling a surge in Covid infections and hospitalisations which have prompted a tightening of domestic restrictions.
The country reported a record daily tally of over 76,000 cases on Friday, with academics and politicians blaming vaccine hesitancy for the surge.
While waning vaccine protection is compounding the emergency, about 3 per cent of Germany’s population have had no Covid vaccine at all - among the highest rates in western Europe.
Much of Germany has already introduced rules to limit access to indoor activities to people who have been vaccinated or have recovered from Covid, but critics say the incoming coalition government needs to act quicker to slow the spread of the virus.