Sony A99 II has a 42.0MP Full frame (35.9 x 24 mm ) sized BSI-CMOS sensor and features Bionz X processor. On the other hand, Nikon D780 has a 25.0MP Full frame (35.9 x 23.9 mm ) sized BSI-CMOS sensor and features Expeed 6 processor.
Sony A99 II's sensor provides 17MP more than Nikon D780'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 Sony A99 II'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 A99 II and D780 sensor size comparison.
Sony A99 II and Nikon D780 have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.