Conducted emissions on the traction battery's power cables in EVs must be limited to avoid unwanted EMI. When designing an EMI filter, it is advantageous to have information of the Common Mode (CM) and Differential Mode (DM) noise levels. This paper deals with the measurement and separation of the DC side's three-wire DM/CM noise of a fault-tolerant threelevel NPC inverter with a split-battery system. Two hardware separators, based on small circuit High Frequency transformers, were developed to identify the DC side's CM, line-DM and phase-DM noise levels. Their characterized CM and DM rejection ratios for the frequency range from 150 kHz to 110 MHz are at least -33 dB and -21 dB, respectively. The separated noise of the NPC inverter was measured, using an inductive load, when operating the inverter with three-level and two-level modulation, resembling normal operation and a possible operation under fault, respectively. A simple three-wire CM model of the used testbed and the DM power module oscillation were derived to validate the separated noise's resonance peaks/valleys. It has been seen that the CM noise is dominant, especially below 10 MHz, except for the power module oscillations. Furthermore, when using the two-level modulation, in case of a clamping diode fault, the noise levels are increased by about 3 dB.