As far as I know, this is done on a per-cell basis (if individual cells have external connections) or for the entire battery.
In any case, a certain load is connected across the cell or battery and the voltage is measured. By measuring both the no-load voltage and the loaded voltage you can easily calculate the internal resistance of the battery
Rbatt=ΔV/I
where ΔV is the difference between the open-circuit voltage and the voltage under load and I is the actual current when the load is connected.
If the battery is in the circuit, you can measure the voltage difference for two different currents, for instance, but you need a way to change the load current and a way to measure accurately the change. Measuring the voltage change is not a problem, a voltmeter will do.