Supply chain (SC) disruptions created due to sustainable, social, economic, environmental and technical risks are mitigated by lean, agile, resilient and green (LARG) capabilities across the SC node. This study aims at the assessment and alignment of SC risks and capabilities for a strategic fit of appropriate practices resulting in performance, efficiency and continuity of operations. The novelty of this research work is the investigation of the direct and mediating effects of strategic system thinking (SST) between SC risks, capabilities and performance. A survey comprising of 78 items was administered to 255 managers of Pakistan automotive SC industries. The exploratory factor analysis and confirmatory factor analysis were executed to identify the valid constructs along with their reliability and validity. The structural equation modeling (SEM) was used to test the conceptual model by establishing the second order constructs. SEM results indicated only technical risks having negative significant effect with performance. In terms of capabilities, the general, efficiency, integration as well as the redundant resources were found to have significant association with SC performance. The SST approach was found to be significantly associated with technical risks and capabilities such as general, recovery and redundancy. The hypothesis of SST as a mediating variable across all factors was not observed to be valid in this research. This study can help in the policy and decision-making as well as strategic assessment, planning, development, positioning and alignment of resources across the sustainable SC. The operations can be influenced positively through system integration and conservation of resources for a sustainable performance. The green, environmental and social risks had higher SC impact and need to be focused upon in Pakistan automotive SC for higher performance and sustainability.