In the last 60 years, auxinic herbicides like 2,4-dichlorophenoxyacetic acid (2,4-D) have been among the widest and successful herbicides used in agriculture because it is a selective herbicide that kills dicots and mimics the natural plant phytohormone indol-3-acetic acid (IAA) at the molecular level. In spite of industry attempts to reformulate 2,4-D-based herbicides and reduce their off-target movement, damage has been reported on sensitive plants, like tomato, at low ratesdi. Therefore, it is important to study the responses of such species to such conditions so that yield losses can be avoided or, at least, reduced. It is known that ethylene, abscisic acid (ABA) and reactive oxygen species (ROS) play a central role in 2,4-D toxicity, leading to numerous unbeneficial changes in plant tissues. Yet, how glutathione-related defense- and/or stress-related genes’ expressions are affected needs to be more studied. In this study, tomato plants (Solanum lycopersicum L.) were used to determine the expression and participation of the different GST phi class gene family members, plus the plans’ antioxidant system, in response to 2,4-D. When tomato plants were root-treated with 2.26 mM 2,4-D for 48 h, H2O2 and O2•− levels increased in shoots. Contrarily, in roots, 2,4-D did not provoke clear symptoms of oxidative stress, as lipid peroxidation, H2O2 and O2•− levels decreased. Despite the difference in ROS levels observed in both organs, the exposure of tomato plants to 2,4-D lead to the activation of key antioxidant enzymes in both organs, apart from superoxide dismutase (SOD), whose activity increased only in roots, while ascorbate peroxidase (APX) and catalase (CAT) activities increased in both. Also, tomato plants responded to 2.26 mM 2,4-D by increasing Ascorbate (AsA) levels in both organs while an increase in Glutathione (GSH) was only observed in shoots. The herbicide increased both the synthesis and the regeneration of GSH, as well as its usage to conjugate 2,4-D, as shoot γ-glutamyl-cysteinyl synthetase (γ-ECS), glutathione reductase (GR) and glutathione S-transferase (GST) activities increased. Shoot GST increased activity was due to an increased expression of SlGSTF4 and SlGSTF5, while no SlGSTFs increased their expression in roots. Shoots and roots of tomato plants were differentially affected by 2.26 mM 2,4-D, with 2,4-D detoxification occurring predominantly in leaves, with the specific participation of the GST phi class members SlGSTF4 and SlGSTF5. Also, this study reinforces the notion that the cultivation of tomato in 2,4-D-contaminated soils may result in yield reduction.