Sony A9 has a 24.0MP Full frame (35.6 x 23.8 mm ) sized BSI-CMOS sensor and features BIONZ X processor. On the other hand, Fujifilm GFX 50S has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features X Processor Pro processor. Fujifilm GFX 50S's sensor provides 27MP more than Sony A9's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Another difference between these two cameras is that Sony A9'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 A9 and GFX 50S sensor size comparison.
As seen above, Fujifilm GFX 50S has a 1.7x Larger sensor area than Sony A9. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.