The change in the relationship between the net photosynthetic rate and stomatal conductance by exposure to ozone is a factor determining cumulative ozone uptake via stomata in Fagus crenata seedlings. Stomatal ozone (O3) uptake, one of the key factors determining the impact of O3 on trees, has been estimated using a coupled model of photosynthesis and stomatal conductance. Exposure to O3 increases or decreases stomatal conductance without changes in the net photosynthetic rate and maximum carboxylation velocity (Vcmax). Such changes in the coupling between photosynthesis and stomatal conductance may be important factors determining stomatal O3 uptake. We aimed to investigate impacts of O3-induced changes in stomatal conductance on the cumulative stomatal O3 uptake of Fagus crenata seedlings grown in three levels of gas treatments: charcoal-filtered air or O3 at 1.0- or 1.5-times the ambient concentration (CF, 1.0 × O3, and 1.5 × O3 treatments, respectively). In July, an O3-induced remarkable reduction in stomatal conductance compared to the net photosynthetic rate (a reduction in the intercept of the Ball–Berry–Leuning model) was observed. Moreover, the exposure to O3 significantly reduced Vcmax during the growing season. Model simulations showed that O3-induced reductions in the photosynthetic capacity, i.e., Vcmax, hardly affect stomatal conductance and cumulative O3 uptake during the growing season. Conversely, the O3-induced remarkable reduction in stomatal conductance compared to net photosynthetic rate in July limited the cumulative stomatal O3 uptake during the growing season by 6% and 10% in the 1.0 × O3 and 1.5 × O3 treatments, respectively. Therefore, we should consider O3-induced changes in the coupling between the net photosynthetic rate and stomatal conductance to calculate the cumulative O3 uptake via stomata of F. crenata using the coupled model.