Internet of Things (IoT) coupled with 5G and upcoming pre-6G networks will provide the scalability and performance required to deploy a wide range of new digital services in Smart Cities. This new digital services will undoubtedly contribute to an improvement in the quality of life of citizens. However, security is a major concern in IoT where low-powered constrained devices are a target for attackers who identify them as a vulnerable entry point to exploit the network weaknesses. This concern is exacerbated in Smart Cities where it is expected to deploy millions of heterogeneous yet unattended and vulnerable IoT devices throughout vast urban areas. A security breach in a Smart City allows attackers to target critical services such as the power grid network or the road traffic control or to expose sensitive health data to intruders. Thus, the security and privacy of citizens could be seriously compromised. Honeynets are an effective security mechanism to distract attackers from legitimate targets and collect valuable information on how they operate. Meanwhile, current honeynets lack functionality to protect the real and lure networks from large-scale volumetric Distributed Denial of Service (DDoS) attacks. This paper provides a novel solution to empower honeynet security tools with Network Slicing capabilities as an innovative way to isolate and minimize the network resources available from attackers. The proposed system supports the ambitious IoT scalability requirements associated to 5G networks and the forthcoming 6G networks. The solution has been empirically evaluated in a emulated testbed where promising results have been achieved when dealing with mMTC and eMBB traffic profiles. In mMTC scenarios where scalability is a challenge, the solution is able to deal with up to 1000 slices and 1 Million IoT devices sending traffic simultaneously. In eMBB use cases, the solution is able to cope with up to 19 Gbps of combined bandwidth. The gathered results demonstrate that the proposed solution is suitable as a security tool in 5G IoT multi-tenant infrastructures as those expected in Smart Cities deployments.