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, Panasonic S1R has a 47.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Venus Engine processor.
Panasonic S1R's sensor provides 21MP more than Fujifilm X-Pro3'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 similarity between these two cameras is that both Panasonic S1R and Fujifilm X-Pro3 sensors lack anti-alias (Low-Pass) filters. 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 S1R sensor size comparison.
As seen above, Panasonic S1R has a 2.4x Larger sensor area than Fujifilm X-Pro3. 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.