Fujifilm S5 Pro has a 6.0MP APS-C (23 x 15.5 mm ) sized CCD sensor . On the other hand, Nikon D6 has a 21.0MP Full frame (35.9 x 23.9 mm ) sized CMOS sensor and features Expeed 6 processor.
Nikon D6's sensor provides 15MP more than Fujifilm S5 Pro'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.
Below you can see the S5 Pro and D6 sensor size comparison.
As seen above, Nikon D6 has a 2.4x Larger sensor area than Fujifilm S5 Pro. 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.