In higher education institutions, digital learning environments, referred to as virtual learning systems in this article, have been adopted and are becoming increasingly popular among academics. A virtual learning system (VLS) has a suite of tools with associated functions and non-functional system characteristics. Higher education institutions (HEIs) implement a VLS with the intent to assimilate e-Learning with face-to-face instruction and thereby derive associated benefits from its usage. Currently there is limited information on educators’ perceptions on the usefulness of VLS tool functionality, and the importance assigned to non-functional characteristics. This article adapted the generic framework of the ISO 9126 external software quality model to ascertain the perceptions of educators with regards to VLS functionality and non-functional quality characteristics. A case study research strategy was adopted, using two South African higher education institutions. The main contribution of this article is a proposed model representing VLS quality in use characteristics, measured by the constructs of perceived usefulness and perceived importance. In addition to the theoretical contribution, this article makes a practical contribution by providing educators’ recommendations on the improvement of VLS quality characteristics. This article has potentially useful implications for the use of a VLS by educators and future VLS design iterations.