Recent literature has raised concerns over crop safety due to nickel (Ni) contamination of irrigation water and agricultural soil in Pakistan. Consequently, wheat crop has suffered in terms of nutrient disbalance and yield reduction. Therefore, it is important to screen tolerant wheat cultivars against Ni toxicity with the ability to accumulate low concentration in grains. In this regard, two wheat cultivars (SKD-1 and Borlaug-16) were exposed to Ni stress (100 mg/L) in a pot experiment for 21 days. In the present study, trace elements (As, Cr, Cu, Cd, Mn, Hg, Ni, Pb, and Zn) and mineral nutrients (Ca, Fe, K, Mg, Na, and P) were tested by ICP-OES. To understand tolerance mechanisms, wheat tissues were tested for morphological parameters, anatomical alteration, oxidative stress, and antioxidant capacity. The translocation of Ni was higher in SKD-1 (0.62) compared to Borlaug-16 (0.45) due to low Ni accumulation in roots of Borlaug-16. In the roots of Borlaug-16, trace elements (Cr, Cu, Mn, Pb, and Zn) were comparatively higher than SKD-1. On the contrary, nutrients (Ca, Fe, Mg, Na, and P) were higher in leaves of SKD-1. Under Ni stress, the root anatomy of Borlaug-16 exhibited a marked increase in the cellular thickness of the cortex by 130.38% and stele by 46.2%. Conversely, the bundle sheath cell thickness rose by 68.36% in the SKD-1. In terms of leaf anatomy, Borlaug-16 showed enhanced thickness in the xylem by 13.01% and bundle sheath cells by 84.95%. Meanwhile, the upper epidermis and phloem of SKD-1 registered thickness increases of 21.80% and 24.47% under Ni stress. Oxidative stress (MDA and H2O2) was comparatively highly induced in SKD-1 tissues compared to Borlaug-16. On the other hand, antioxidants (SOD, CAT, and APX) were comparatively higher in root and leaf tissues of Borlaug-16. The lower Ni uptake, less cellular damage, and high antioxidant capacity of Borlaug-16 makes it more tolerant to Ni stress. Such findings will pave the way towards sustainable crop production.