The effect of three rootstocks on the responsiveness of “Superior Seedless” grapes to cold storage was investigated in this study during the growing seasons of 2021 and 2022. The “Superior Seedless” bunches were preserved for 90 days at 4 ± 1°C and 98 ± 2 relative humidity%. The “Superior Seedless” bunch response under cold storage was shown to be influenced by the rootstocks. According to the study, bunches picked from “Superior Seedless” that were grown on the “1103 Paulson” rootstocks performed better in antioxidant enzyme activities (AEAs) than bunches obtained from other rootstocks. Furthermore, during cold storage, the rates of H₂O₂ and O₂⁻generation decreased more rapidly. However, combined with a low electrolyte leakage percentage (EL%) and malondialdehyde (MDA) accumulation, the 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenger concentration increased during the cold storage period. Furthermore, while berry quality traits were harvested from “Superior Seedless” grafted onto “1103 Paulson” rootstock, they were improved compared to other rootstocks. The molecular docking technique is performed to evaluate the binding affinity of antioxidant enzymes with a group of intracellular ligands, including DPPH, MDA, ascorbic acid, and tartaric acid, which show great results with respect to the DPPH compound. Following these findings, it can be concluded that the influence of rootstocks on “Superior Seedless” bunch responses to low cold storage represents a novel potential natural effect of rootstocks on responding bunches of “Superior Seedless” to low cold storage.