Matisse's "Woman Sitting in an Armchair" was part of a trove of artworks found in the apartment of late collector Cornelius Gurlitt.
Experts say the painting was taken from art dealer Paul Rosenberg and rightfully belongs to his descendants.
Culture Minister Monika Gruetters' office confirmed a report in German daily Frankfurter Allgemeine Zeitung Wednesday that she signed the agreement.
A similar agreement was signed last week for a painting by Max Liebermann.
Both agreements must be approved by a Munich court handling Gurlitt's inheritance.
A Swiss museum that accepted Gurlitt's bequest of his collection has promised to ensure any Nazi-looted pieces are returned to their Jewish owners' heirs.