The wide expansion of digital technologies in higher education has introduced the need for an examination of the added value of various technological tools for quality teaching and active individual and collaborative learning. The current study explored whether and how the pedagogical design of an academic course, which developed a variety of digital literacy competencies, supported students in regulating collaborative technology-enhanced learning and helped them cope with the sense of psychological ownership over collaborative learning outcomes. In addition, we examined how these issues were expressed in cognitive, emotional and social aspects of students' perceived learning (Caspi & Blau, 2011). During four semesters, we conducted a qualitative analysis on reflective learning diaries, written by 78 graduate students studying education (N = 1870 codes). The bottom-up analysis focused on learning processes that enabled the development of various digital literacies conceptualized by the Digital Literacy Framework (DLF; Eshet-Alkalai, 2012): photo-visual, information, reproduction, branching, social-emotional, and real-time thinking skills. Furthermore, findings highlighted the importance of self-regulation and learning new technologies as an integral part of digital literacies. In addition, social-emotional statements expressed the development of effective communication and collaboration that enable students to cope with a sense of ownership over learning outcomes, and present different levels of teamwork: sharing, cooperation, and collaboration. Qualitative coding provided a more granulated perspective on perceived learning by differentiating between positive and negative aspects of emotional and social retrospection during the learning process. The findings contribute to educational theory by extending DLF and by providing new insights to the literature on students' perceived learning. We discuss the implications for instructional design and adoption of innovative pedagogy in higher education.