COVID-19 has posed many unique and critical challenges in various contexts and circumstances. This often led the stakeholders and decision-makers to depart from traditional thinking and the business-as-usual processes and to come up with innovative approaches to tackle various mission-critical situations within a short time frame. In this paper, a real-life case study of COVID-19 operation management following a multi-disciplinary, multi-stakeholder novel integrated approach in aged care facilities in Victoria, Australia, is presented which yielded significant and positive outcomes. The purpose of the intervention was to develop an integrated system performance approach through the application of various quality management tools and techniques to achieve organizational excellence at the aged care centers. The case involved the use of mathematical models along with statistical tools and techniques to address the specific problem scenario. A system-wide management plan was proposed, involving various agencies across several residential aged care facilities during the pandemic. A three-step methodological framework was developed, where Six Sigma, a system thinking approach, and a holistic metric were proposed to manage the value chain of the pandemic management system. The experimental result analyses showed significant improvement in the management process, suggesting the validity and potential of this holistic approach to stabilize the situation and subsequently set the conditions for operations excellence within the sectors. The model offers new insight into the existing body of knowledge and offers an efficient approach to achieving operational excellence in any organization or business regardless of its type, shape and complexity, which can help practitioners in managing complex, mission-critical situations like a pandemic.