The decision was made late on Wednesday evening in light of high infection rates in the two French-speaking cantons, reports Swiss news outlet 20 Minutes.
The result of the decision is that anyone who enters from either Geneva or Vaud must be tested on arrival in Germany.
This applies to returning German citizens as well as any other arrivals from a high-risk area.
The tested person must then quarantine until the test result comes through, relying on health authorities for guidance.
Germany's threshold for placing a country on the high-risk list is 50 infections per 100,000 residents over the previous seven days.
Geneva and Vaud, along with Zurich, have the countries highest rates of new infections. The three have been nicknamed Switzerland's 'problem cantons' by Swiss media.
As yet, there is no plan to include Zurich on Germany's travel warning list.