During the SARS-CoV-2 (COVID-19) pandemic, many countries have struggled to provide definitive guidance on ways to reduce the highly infectious transmission of the virus within indoor and other environments where there are more people contained within a shared air volume. Yet the engineering of pandemic related mitigations required multiple domains and disciplines to rapidly execute on scientific discovery and evidence-based decisions balanced with supply availability and practicality – all of which have made this a challenging Systems Engineering problem. In this presentation, we discuss the concepts of using observable phenomena as a basis for theoretical foundations that enable evidence-based systems engineering and model-based systems engineering for reducing COVID-19 aerosol transmission risks. We will share our story of rapidly applying systems engineering to several real-life pandemic scenarios and field experiments on reducing the airborne dispersion of aerosolized particles from exhalation. We will also share our experiences on the emerging need to develop reusable models and practical system engineering frameworks for reducing aerosol risks and present a use-case of applying MBSE and evidence-based systems engineering to reduce COVID-19 aerosol transmission risks at the southern U.S. border and in schools.