Soybean (Glycine max (L.) Merr.) is one of the most economically important crops in the world due to its nutritional value. To optimize soybean growth and yield, a wide range of commercial herbicides intended for weed control in crops are used. Although the herbicides used are selective, they can still cause oxidative stress and disturb photosynthetic reactions in soybean crops. In this work, the influence of commercial selective herbicides for weed control on the photosynthetic efficiency and antioxidative response of two soybean cultivars was investigated. The parameters describing the photosynthetic performance of soybean were derived by measuring in vivo chlorophyll a fluorescence while the antioxidative response was evaluated by determining activities of the selected antioxidative enzymes and parameters of oxidative stress at different development stages. The results showed a different response of the two soybean cultivars to herbicide treatment. Both investigated soybean cultivars showed that herbicide treatment did not cause oxidative damage. However, they revealed different adaptation mechanisms of photosynthetic apparatus. A negative impact of herbicide application was observed mainly on the electron transport chain in both varieties.