Farmers around the world are concerned about the effects of human-induced salinity on crop yield and quality. Therefore, researchers are actively testing wild relatives of cultivated plants to identify candidates to improve crop performance under salt stress. A study was conducted to understand the effects of salt stress (Sodium chloride, NaCl) on cultivated tomato species (Solanum lycopersicum var. cerasiforme L.) and a wild tomato relative (Solanum chilense Dun.) from the Northern part of Chile. Plants were cultivated hydroponically under controlled environmental conditions for 112 days with nutrient solution containing 0 mM (3 dS m−1), 40 mM (6 dS m−1) and 80-mM (9 dS m−1) NaCl. Salt stress reduced the shoot biomass in S. lycopersicum but not in S. chilense. Both species were able to maintain the leaf water content; however, the cultivated S. lycopersicum showed osmotic adjustment, while S. chilense did not. Salt stress reduced the total fruit yield in S. lycopersicum based on a decrease in the mean fruit weight, but it had no impact on the number of fruits per plant. In contrast, salt stress had no significant impact on the fruit yield in S. chilense. Salt stress increased the total soluble solids content in S. lycopersicum and the titratable acidity in S. chilense. It was concluded that S. chilense displays a contrasting behaviour in response to prolonged exposure to moderate salinity compared with S. lycopersicum, and that this related species could be an interesting plant for breeding purposes.