Contamination of soil with heavy metals is a worldwide problem, which causes heavy metals to release into the environment. Remediation of such contaminated soil is essential to protect the environment. The aims of this study are: first, to compare the effect of biochar and the joint application of biochar with fertilizer for the phytoremediation of heavy metals-contaminated soil using Acacia auriculiformis; second, to study the effect of the application rate of biochar in improving the physicochemical properties of the soil. The soil samples were collected from an active coal mine dump and assessed for their physicochemical properties and heavy metals toxicity. Initial results indicated that the soil has poor physicochemical properties and was contaminated with the presence of heavy metals such as Zn, Ni, Cu, Cr, and Co. Later, the heavy metals-contaminated soil was mixed with the 400 and 600 °C biochar, as well as the respective biochar–fertilizer combination in varying mixing ratios from 0.5 to 5% (w/w) and subjected to a pot-culture study. The results showed that the application of both varieties of biochar in combination with fertilizer substantially improved the physicochemical properties and reduced the heavy metals toxicity in the soil. The biochar and fertilizer joint application also substantially improved the soil physiochemical properties by increasing the application rate of both varieties of biochar from 0.5 to 5%. The soil fertility index (SFI) of the biochar and biochar–fertilizer amended soil increased by 49.46 and 52.22%, respectively. The plant’s physiological analysis results indicated a substantial increase in the plant’s shoot and root biomass through the application of biochar and biochar–fertilizer compared to the control. On the other hand, it significantly reduced the heavy metals accumulation and, hence, the secretion of proline and glutathione hormones in the plant cells. Therefore, it can be concluded that the joint application of biochar with the application rate varying between 2.5 to 5% (w/w) with the fertilizer significantly improved the physicochemical properties of the soil and reduced the heavy metals toxicity compared to the controlled study.