We demonstrate a transformational technique for controllably tuning the electrical properties of individual aluminum-oxide tunnel junctions. Using conventional test equipment to apply an alternating bias to a heated tunnel barrier, giant increases in the room temperature resistance, greater than 70%, can be achieved. The rate of resistance change is shown to be strongly temperature- dependent, and is weakly dependent on junction size in the sub-micron regime. In order to measure their tunneling properties at mK temperatures, we characterized transmon qubit junctions treated with this alternating-bias assisted annealing (ABAA) technique. The measured frequencies follow the Ambegaokar-Baratoff relation between the shifted resistance and critical current. Further, these studies show a reduction of junction-contributed loss on the order of ≈ 0.3 × 10−6, and indicate that there is a reduction in resonant-and off-resonant-two level system defects when compared to untreated samples. Imaging with high-resolution TEM shows that the barrier is still predominantly amorphous with a more uniform distribution of aluminum coordination across the barrier relative to untreated junctions. This new approach is expected to be widely applicable to a broad range of devices that rely on amorphous aluminum oxide, and is likely applicable to many other metal- insulator-metal devices.