Photosynthesis by trees is expected to contribute to preventing climate change including global warming. However, the current levels of tropospheric ozone (O3) reduce the uptake of photosynthetic carbon dioxide (CO2) by forest trees in Japan, which is a concern. Furthermore, it is unknown how much O3 should be reduced to prevent plants’ O3-induced damage. The objective of the present study was to assess the negative effects of the current levels of O3 absorbed via stomata and the impact of its mitigation on the CO2 uptake by trees in Japanese forests. Impact assessment, targeted in 2011–2015, was performed for four deciduous broad-leaved trees: Fagus crenata, Quercus serrata, Q. mongolica var. crispula, and Betula platyphylla var. japonica. The assessment was based on species-specific cumulative stomatal O3 uptake (COU) and species-specific responses of annual photosynthetic CO2 uptake to COU. Annual COU differed between the four trees; the average COU of F. crenata, Q. serrata, Q. mongolica var. crispula, and B. platyphylla var. japonica across Japan was 41.7, 26.5, 33.0, and 29.1 mmol m−2, respectively, and the reductions in CO2 uptake by the four trees were 14.0%, 10.6%, 8.6%, and 15.4%, respectively. Further analysis revealed that reducing the atmospheric O3 concentration by approximately 28%, 20%, 17%, and 49% decreased the O3-induced reductions in photosynthetic CO2 uptake to 5% in F. crenata, Q. serrata, Q. mongolica var. crispula, and B. platyphylla var. japonica, respectively. In the near future, implementing mitigation measures for the O3 damage in plants is expected to enhance the photosynthetic capacity of Japanese forest tree species.