Influences from the modern business environment indicate the need for the incorporation of sustainability concepts from an innovation system perspective. In the presented research, we emphasize the energy efficiency concept within the frame of sustainability and innovation. The aim of this research was to underline and explore the relationships between innovation, energy efficiency, and sustainability in the construction industry. To answer the research questions, a questionnaire was created to explore the impact of the energy efficiency certification process on the innovation behavior of construction industry enterprises in Serbia. The results show that energy efficiency has supported innovation, and that there exists a relationship between sustainability and innovativeness in the construction industry. Applying energy efficiency passports has influenced the co-operation of enterprises in the construction sector and other actors in the national innovation system in Serbia. The innovation concept demonstrates that enterprises in the construction industry should be observed as a part of the wider picture—the national innovation system. In turn, the specific context of a particular national innovation system should be seen within the wider picture of national innovation systems of Central and Eastern European Countries (CEECs).