This study investigated the effects of green and red photo-selective filters (shade nets) on the process of graft union formation (healing and acclimation) in grafted tomato plants. The research evaluated oxidative stress, physiological characteristics, and anatomical development of graft unions. Plants were subjected to green-netting, red-netting, and no-netting treatments for 28 days, starting 4 days after grafting. Markers of oxidative stress, including reactive oxygen species (ROS), superoxide dismutase (SOD), peroxidase (POD), and malondialdehyde (MDA), as well as protein concentration of SOD/POD enzyme-enriched extracts, were quantified. The anatomical development of the graft unions was examined using microscopy. The results demonstrated that the red and green photo-selective filters increased ROS production by 5% and 4% after 3 days of exposure, by 58% and 14% after 7 days, and by 30% and 13% after 14 days in comparison to the control treatment. The increase in ROS activates the defense mechanism, enhancing the activity of SOD and POD enzymes. In terms of anatomy, the green netting resulted in enhanced cell proliferation and early differentiation of vascular tissue cells. Notably, at the 28-day mark, when the plants were ready for transplanting, the green-net treatment showed a reduction in lipid peroxidation damage and increases of 20% and 54% in dry weight compared with the control and red-net treatments, respectively. Finally, our results suggest that the use of a green photo-selective filter has a positive effect on oxidative stress, anatomical development, and overall growth of grafted tomato plants during the process of graft union formation.