You can't directly measure the internal resistance of the battery with the DMM. There are two ways to measure internal battery resistance.
1) Use an industry standard 1KHz battery impedance meter. They go from around 50-60 bucks out of China up to thousands for a real good one. I found the cheaper models from China seem to do a good job and they are even 4-wire.
2) Use 2 meters, such as your Agilent and another DMM. Measure current on one with .5A, 1A and maybe 1.5A depending on your battery. You can use an electronic load for this if you have one or just a power resistor that can handle the current. Use the other DMM to measure the voltage drop across your battery
For step 2, make sure you select a resistor that will not discharge the cell to quickly. Typically around 1A for 18650's and .5A for smaller cells.
First, measure the cell voltage in an open circuit. (Nothing connected), then measure the resistor you are using. Next, connect the load resistor and battery to make a complete circuit. Measure the voltage drop across the battery, then subtract the open circuit voltage across the battery to the loaded circuit voltage across the battery and subtract to get the difference. Also make note of the current during the loaded test. Then use ohms law to calculate the internal resistance of the battery.
Here is an example I did with an old 18650:
1) Measure open circuit voltage across battery. (3.883V)
2) Connected 4.7 Ohm load across battery, measured both current and voltage drop across battery. (3.625V) and (690mA)
3) Subtract (3.883)-(3.625) = (0.258), this is your voltage drop across the battery.
4) Use Ohms law to calculate resistance: Resistance (R) = Voltage (V)/ Current (I). So (.258) / (.690) = .373913 or 373.913 mOhm.
A typical GOOD Lion cell like an 18650 should have an internal resistance of around 60 to 100 mOhms. The cell above is worn and at lifes end which is typical for an 18650 that is 8+ years old with hundreds of cycles to be higher in internal resistance. Keep in mind this is a DC resistance test and many prefer this over a 1KHz AC impedance test. I choose to do both methods and compare the results.
Hope this helps!