Sony A6400 has a 24.0MP APS-C (23.5 x 15.6 mm ) sized CMOS sensor and features Bionz X 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 23MP more than Sony A6400'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 A6400 and S1R sensor size comparison.
As seen above, Panasonic S1R has a 2.4x Larger sensor area than Sony A6400. 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.
DxOMark Sensor Scores
DxOMark is a benchmark that scientifically assesses image quality of camera sensors. It scores camera sensors for color depth (DXO Portrait), dynamic range (DXO Landscape) and low-light sensitivity (DXO Sports), and also gives them an overall score. Sony A6400 and Panasonic S1R sensors have been tested by DxO and the results show that S1R has a better overall score of 100, 17 points higher compared to A6400's score of 83.