Fujifilm X-Pro3 has a 26.0MP APS-C (23.5 x 15.6 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Leica CL has a 24.0MP APS-C (23.6 x 15.7 mm ) sized CMOS sensor and features Maestro II processor.
Another difference between these two cameras is that Fujifilm X-Pro3's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the X-Pro3 and CL sensor size comparison.
Fujifilm X-Pro3 and Leica CL have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.