I've confirmed that the Gigabyte GA-Z97N manual says what you've written about the CPU and SYS fan headers but I would guess that the SYS fan header information is wrong (it wouldn't be the first time!).
According to Wikipedia's "Computer fan control" page, "...cooling fans used in computers use standardized connectors with two to four pins. The first two pins are always used to deliver power to the fan motor, while the rest can be optional, depending on fan design and type". It further states that the 'Power' (pin 2) pin is "nominally +12 V, though it may be variable depending on fan type and desired fan rotation speed".
I've read elsewhere that a common SYS fan pinout is: "GND, Fan Power, Fan RPM Sense, +5V (no PWM fan-speed control)". I suspect this is what Gigabyte meant to print in their manual (with +12V or +5V in place of "Fan Power").
I'll bet there is continuity (0 ohms) between pin 2 of the CPU fan header and pin 2 of the SYS fan header (+12V). If no +12V continuity, check for continuity between pin 2 of the SYS fan header and a known +5V source such as pin 4 of the 24-pin power supply header. If no continuity from pin 2 of the SYS fan header to either +12V or +5V, it would suggest that the Gigabyte manual might be right after all (doubtful).
I have also found that the CoolerMaster Nepton 120XL is looking for +12V for both the fan and the pump (per ocdrift.com's CoolerMaster Nepton 120XL review). Note: You want PWM control for both the fan and the pump so they aren't running at full speed all the time.
You should be fine using the splitter as the generally accepted rule with fan headers is all headers combined can deliver 1A of current (or 12W at 12V). When running at 100%, the pump uses about 4.8W (0.4A) and the fan pulls about the same amount of current for a total of 0.8A.