Presented are vehicle control systems and logic for monitoring device batteries to provision virtual key functionality, methods for making/using such systems, and vehicles equipped with such systems. A method of operating a vehicle includes wire or wirelessly connecting a remote keyless entry (RKE) system with a wireless-enabled portable electronic device (PED) of a user. A vehicle controller receives a unique virtual key code from the user's PED to enable use of the RKE system and, after receiving the virtual key code, determines a battery charge level of the PED's battery. The vehicle controller then determines if the battery charge level is less than a preset minimum charge level and if the vehicle powertrain is off. If the powertrain is off and the battery charge level is less than the minimum charge level, the controller responsively commands a resident vehicle subsystem to execute a control operation for charging the PED battery.