The transformation of society towards digitalization and automatization cannot be ignored by the higher education system. While this has been naturally reflected by the education system regarding technical sciences, humanities are still struggling to catch up with the latest trends in the digitalization of society. The field of Digital Humanities (DH) is very young and lacks a solid methodological basis or ontological principles. This paper aims at proposing some philosophical and methodological grounding for the field of DH and its practical applications in the higher education system. We describe two case studies of the creation of new study programs at the Palacký University Olomouc, Czech Republic.