Praying Virgin, 17 x 22in (44 x 56cm), dates to 1552 and comes from a German collection.
It depicts the Virgin Mary dressed in a cloak (once blue but now faded to brown) and a semi-transparent veil. Typically for Matsys, her copper-coloured hair is rendered with parallel golden lines.
The painting is set to be included in the forthcoming catalogue raisonné on Matsys edited by Maria Clelia Galassi.
Born in Antwerp, son of well-known painter Quinten Matsys, the artist is known for his history and genre paintings as well as depictions of the female nude.
The Virgin appears in other works by the artist at the Prado and the Museo Lázaro Galdiano in Madrid.
The acquisition was made with a contribution from the Benedicti Claustra Onlus branch of the abbey, which had been seeking a Flemish work for its permanent collection.
The price was not disclosed.