When two batteries are connected in parallel, positive to positive and negative to negative, the circuit is completed. In this circuit, one battery serves as a load for another. The direction of the current will depend on which battery has a higher voltage. The current in such circuit will be limited by internal resistance of the batteries.
The equalization of the voltages occurs due to a voltage drop on the internal resistance of the dominant battery, not due to the re-distribution of the terminal charges, which, as you've pointed out, don't amount to much.