The world is experiencing a rapid growth of smart cities accelerated by Industry 4.0, including the Internet of Things (IoT), and enhanced by the application of emerging innovative technologies which in turn create highly fragile and complex cyber–physical–natural ecosystems. This paper systematically identifies peer-reviewed literature and explicitly investigates empirical primary studies that address cyber resilience and digital forensic incident response (DFIR) aspects of cyber–physical systems (CPSs) in smart cities. Our findings show that CPSs addressing cyber resilience and support for modern DFIR are a recent paradigm. Most of the primary studies are focused on a subset of the incident response process, the “detection and analysis” phase whilst attempts to address other parts of the DFIR process remain limited. Further analysis shows that research focused on smart healthcare and smart citizen were addressed only by a small number of primary studies. Additionally, our findings identify a lack of available real CPS-generated datasets limiting the experiments to mostly testbed type environments or in some cases authors relied on simulation software. Therefore, contributing this systematic literature review (SLR), we used a search protocol providing an evidence-based summary of the key themes and main focus domains investigating cyber resilience and DFIR addressed by CPS frameworks and systems. This SLR also provides scientific evidence of the gaps in the literature for possible future directions for research within the CPS cybersecurity realm. In total, 600 papers were surveyed from which 52 primary studies were included and analysed.