Tomato mosaic disease, caused by tomato mosaic virus (ToMV), was studied under naturally elevated [CO2] concentrations to simulate the potential impacts of future climate scenarios on the ToMV–tomato pathosystem. Tomato plants infected with ToMV were cultivated under two distinct [CO2] environments: elevated [CO2] (naturally enriched to approximately 1000 μmol mol−1) and ambient [CO2] (ambient atmospheric [CO2] of 420 μmol mol−1). Key parameters, including phytopathological (disease index, ToMV gene expression), growth-related (plant height, leaf area), and physiological traits (chlorophyll content, flavonoid levels, nitrogen balance index), were monitored to assess the effects of elevated [CO2]. Elevated [CO2] significantly reduced the disease index from 2.4 under ambient [CO2] to 1.7 under elevated [CO2]. Additionally, viral RNA expression was notably lower in plants grown at elevated [CO2] compared to those under ambient [CO2]. While ToMV infection led to reductions in the chlorophyll content and nitrogen balance index and an increase in the flavonoid levels under ambient [CO2], these physiological effects were largely mitigated under elevated [CO2]. Infected plants grown at elevated [CO2] showed values for these parameters that approached those of healthy plants grown under ambient [CO2]. These findings demonstrate that elevated [CO2] helps to mitigate the effects of tomato mosaic disease and contribute to understanding how future climate scenarios may influence the tomato–ToMV interaction and other plant–pathogen interactions.