Fujifilm GFX 100 has a 102.0MP Medium format (44 x 33 mm ) sized BSI-CMOS sensor and features X-Processor 4 processor. On the other hand, Panasonic S1R has a 47.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Venus Engine processor.
Fujifilm GFX 100's sensor provides 55MP more than Panasonic S1R'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.
One other difference between these two cameras that is worth mentioning is that Panasonic S1R's sensor doesn't have an 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 100 and S1R sensor size comparison.
As seen above, Fujifilm GFX 100 has a 1.7x Larger sensor area than Panasonic S1R. 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.