One of the major issues which are hindering widespread and seamless adoption of Internet of Thing (IoT) is security. The IoT devices are vulnerable and susceptible to attacks which became evident from a series of recent large-scale distributed denial-of-service (DDoS) attacks, leading to substantial business and financial losses. Furthermore, in order to find vulnerabilities in IoT, there is a lack of comprehensive security analysis framework. In this paper, we present a modular, adaptable and tunable framework, called PIT, to probe IoT systems at different layers of design and implementation. PIT consists of several security analysis engines, viz., penetration testing, fuzzing, static analysis, and dynamic analysis and an exploitation engine to discover multiple IoT vulnerabilities, respectively. We also develop a novel grey-box fuzzer, called Applica, as a part of the fuzzing engine to overcome the limitations of the present day fuzzers. The proposed framework has been evaluated on a real-world IoT testbed comprising of the state-of-the-art devices. We discovered several network and system-level vulnerabilities such as Buffer Overflow, Denial-of-Service, SQL Injection, etc., and successfully exploited them to demonstrate the presence of security loopholes in the IoT devices.