Aluminum (Al) toxicity in acidic soils is a major abiotic stress that negatively impacts plant growth and development. The toxic effects of Al manifest primarily in the root system, leading to inhibited root elongation and functionality, which impairs the above-ground organs of the plant. Recent research has greatly improved our understanding of the applications of small molecule compounds in alleviating Al toxicity. This study aimed to investigate the role of boron (B), silicon (Si), and their combination in alleviating Al toxicity in soybeans. The results revealed that the combined application significantly improved the biomass and length of soybean roots exposed to Al toxicity compared to B and Si treatments alone. Our results also indicated that Al toxicity causes programmed cell death (PCD) in soybean roots, while B, Si, and their combination all alleviated the PCD induced by Al toxicity. The oxidative damage induced by Al toxicity was noticeably alleviated, as evidenced by lower MAD and H2O2 accumulation in the soybean roots treated with the B and Si combination. Moreover, B, Si, and combined B and Si significantly enhanced plant antioxidant systems by up-regulating antioxidant enzymes including CAT, POD, APX, and SOD. Overall, supplementation with B, Si, and their combination was found to alleviate oxidative damage and reduce PCD caused by Al toxicity, which may be one of the mechanisms by which they alleviate root growth inhibition due to Al toxicity. Our results suggest that supplementation with B, Si, and their combination may be an effective strategy to improve soybean growth and productivity against Al toxicity.