Presented are traction battery pack balancing systems, methods for making/operating such systems, and multi-pack, electric-drive motor vehicles with battery pack balancing capabilities. A method for controlling operation of a motor vehicle includes a vehicle controller: receiving a key-off command signal to power off the motor vehicle; determining if a difference between corresponding electrical characteristics of first and second traction battery packs is greater than a calibrated characteristic differential threshold; determining if a difference between corresponding battery pack capacities of the first and second traction battery packs is greater than a calibrated capacity differential threshold; and, responsive to the characteristic difference not being greater than the calibrated characteristic differential threshold and the capacity difference being greater than the calibrated capacity differential threshold, transmitting a key-on command signal to power on the motor vehicle, and a pack balancing command signal to reduce the capacity difference to below the calibrated capacity differential threshold.