Salinity is one of the most critical crises worldwide that ultimately compromises future food security. Brassinosteroids including brassinolide (BL) are a class of polyhydroxy steroids phytohormones, that play a crucial role in several plant metabolic pathways and boost plants’ stress tolerance, but less data is accessible on its function in salt-affected grapevine. The experiment was conducted throughout the 2019 and 2020 experimental seasons at EL-Baramon experimental farm, Horticulture Research Institute, Mansoura, Egypt, to recognize the remediation potential of BL (1 and 2 mg L−1) in lightening salinity (NaCl at 1000, 2000, and 3000 mg L−1) injury on Thompson seedless grapevine seedlings (H4 strain) growth and physio-anatomical attributes. Data advocated that while salinity reduced growth attributes, BL applications substantially improved the overall salt-affected plant performance. Salinity stress significantly decreased photosynthetic pigment, relative water content, and ions percentage (nitrogen, phosphorus, potassium, potassium/sodium ratio). Alternatively, BL spraying significantly (p ≤ 0.05) increased the photosynthetic pigment, maintaining a favorable potassium/sodium ratio and increasing the ions percentage. Additionally, increasing salinity levels significantly boost plant sodium percentage and induce a membrane malfunction associated with increased membrane permeability; conversely, the application of BL decreased the sodium percentage associated with decreasing membrane permeability relative to non-treated salinized plants. Moreover, salinity and/or BL significantly improved the antioxidant capacity associated with rising proline accumulation and antioxidant enzyme activities. Anatomically, salinity stress considerably modified leaf structure; meanwhile, the spraying with BL drastically mitigates the harmful effects of salinity on leaf anatomy. Additionally, salt-affected plant cells explained various obvious organelles ultrastructural modifications and cellular damage; meanwhile, BL spraying to salt-affected plants repealed the ultrastructural modifications of cell organelles. Taken together, BL, especially 2 mg L−1, has a great potential to boost the salt tolerance of Thompson seedless grapevine seedlings (H4 strain). It improves salt tolerance by sustaining higher photosynthetic pigment concentrations, maintaining ion homeostasis, regulating water status, and stimulating antioxidant capacity as well as maintaining leaf anatomical attributes.