This study aims to determine grafting’s efficiency to improve tomato growth and production under salinity stress conditions. A commercial tomato hybrid (cv. Bark) and eight wild tomato accessions were evaluated at molecular, physiological and agronomic levels. At the molecular level, two robust gene-targeting marker systems (Conserved DNA-Derived Polymorphism; CDDP and Start Codon Targeted Polymorphism; SCoT) were employed. Bark cv. was grafted as a scion onto the four tomato genotypes’ roots as stocks. The rootstocks effect was evaluated by growing plants at 0, 100 and 200 mM NaCl. Our results showed that grafting enhanced plant shoots and roots growth (plant height, number of branches, plant fresh weight, root length, and root fresh and dry weight), fruit yield (total yield, number and weight of fruits) and fruit quality (Vitamin C, firmness and total soluble solids) in Bark on most tested rootstocks. A significant interaction between salinity levels and rootstocks for all measured hormones, antioxidants and proline was observed. In conclusion, our consistent results from the three approaches (molecular, physiological and agronomical) revealed that the four genotypes (LA1995, LA2711, LA2485 and LA3845) were found to be grouped and exhibit better performance under salinity stress conditions. Furthermore, grafting could be a low-cost alternative method to improve salt tolerance in sensitive tomato genotypes.