Aluminum is one of the most important heavy metals inducing stress during plant growth and development. In this study, transgenic rice (Oryza sativa L., cv. Kitaake) plants expressing the maize C4PEPC and PPDK genes were evaluated for aluminum tolerance. A 4.3 and 19.1 folds increase of PPDK and PEPC activities in transgenic rice produced increases in root exudation of oxalate, malate, and citrate (1.20, 1.41, and 1.65 times, respectively) compared to untransformed (WT) plants. Transgenic rice had enhanced aluminum tolerance compared to WT based on chlorophyll fluorescence and chlorophyll levels. Transgenic plants under aluminum stress also had decreased lipid membrane oxidative damage and higher levels of ROS-scavenging enzyme activity. The PEPC and PPDK genes play an important role in aluminum stress tolerance by increasing the effluxes of organic acids.