Dialectics, or developmental transformation, would eventually cause any system to change. The level and depth of these changes vary and depend on the power of external influence and system reservation mechanisms. The art of managing system processes consists of two main aspects. The first aspect involves the sagacity of managers and predicting general environmental change trends (and their impacts on the managed system). The second involves adjusting to these trends, maximizing possible benefits, and minimizing the negative manifestations of this process. Innovation plays an important role, contributing to system transformations with maximal effect and minimal loss. Public transport systems are important elements in cities, as they provide spatial mobility for at least half of the citizens of a city who cannot use individual transportation. Modern urbanization and peculiarities of the social–economic statuses of many citizens contribute to the fact that organized public transportation is unprofitable. The low solvency of citizens who use public transportation services means that passenger transport systems do not work with enough profitability. As a result, governing institutions often choose to subsidize unprofitable transporter activities, thereby prolonging the functioning of unprofitable routes. This is possible only in conditions of sustainability (in regards to a non-optimal system), when the environment is calm, and its negative impact is low. “Black swans” (according to N. Taleb) are bifurcation factors that break the sustainability of non-optimal system. Urban public transport (UPT) of a large Russian city, Tyumen, experienced it in 2020, in connection with the COVID-19 lockdown. The sharp decrease in population mobility in Tyumen, in 2020–2021, caused the need for a complete transformation of the transport service system. However, managers did not want to fundamentally change a system that consensually suited most counterparties. The search for new balances in a system that demands transformation is one way for sustainable provision. This article looks at the transformation and sustainability of a UPT system in the large Russian city of Tyumen, under conditions affected by the negative impact of COVID-19. Results of a comparative (i.e., pre-crisis (2019) and crisis (2020)) Pareto analysis of the contributions of different UPT routes are presented. Transformation of the structure of the UPT route system can overcome the “crisis” COVID-19 period and minimize its financial-economic costs.