Nikon D800E has a 36.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features Expeed 3 processor. On the other hand, Fujifilm GFX 50R has a 51.0MP Medium format (44 x 33 mm ) sized CMOS sensor and features X Processor Pro processor.
Fujifilm GFX 50R's sensor provides 15MP more than Nikon D800E'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 Nikon D800E'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 D800E and GFX 50R sensor size comparison.
As seen above, Fujifilm GFX 50R has a 1.7x Larger sensor area than Nikon D800E. 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.