Fujifilm GFX 50S has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features X Processor Pro processor. On the other hand, Sony A99 II has a 42.0MP Full frame (35.9 x 24 mm ) sized BSI-CMOS sensor and features Bionz X processor. Fujifilm GFX 50S's sensor provides 9MP more than Sony A99 II'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 A99 II'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 GFX 50S and A99 II sensor size comparison.
As seen above, Fujifilm GFX 50S has a 1.7x Larger sensor area than Sony A99 II. 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.