Nikon D800 has a 36.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features Expeed 3 processor. On the other hand, Sony A99 has a 24.0MP Full frame (35.8 x 23.8 mm ) sized CMOS sensor and features Bionz processor.
Nikon D800's sensor provides 12MP more than Sony A99'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 D800 and A99 sensor size comparison.
Nikon D800 and Sony A99 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.
DxOMark Sensor Scores
Both Nikon D800 and Sony A99 sensors have been tested by DxoMark. DxoMark 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. Of the two cameras that we are comparing, D800 has scored 95, 6 points higher than A99.