Both Sony A6500 and Fujifilm X-E3 have 24.0 MP resolution sensors but Sony A6500's sensor is APS-C (23.5 x 15.6 mm ) and Fujifilm X-E3's sensor is APS-C (23.6 x 15.6 mm ).
Since Fujifilm X-E3's has a larger sensor area with the same resolution, this means that it also has a larger pixel area hence better light collecting capacity for a given aperture compared to Sony A6500.
Another difference between these two cameras is that Fujifilm X-E3'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 A6500 and X-E3 sensor size comparison.
Sony A6500 and Fujifilm X-E3 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.