The rapid growth of Information Communication Technologies (ICT) has impacted many fields. In this context, the supply chain has also quickly evolved toward the digital supply chain where digital and electronic technologies have been integrated into every aspect of its end-to-end process. This evolution provides numerous benefits such as profit maximization, loss reduction, and the optimization of supply chain lead times. However, the use of such technologies has also considerably opened up various security threats and risks which have widened the attack surface on the entire end-to-end supply chain. We present a holistic survey on supply chain security. We discuss the different security issues and attacks that target the different supply chain technologies. Then, we discuss various countermeasures and security solutions proposed by academic and industry researchers to mitigate the identified threats. Finally, we provide some recommendations and best practices that can be adopted to achieve a secure supply chain.