Both Fujifilm X-Pro2 and Sony A99 have 24.0 MP resolution sensors but Fujifilm X-Pro2's sensor is APS-C (23.6 x 15.6 mm ) and Sony A99's sensor is Full frame (35.8 x 23.8 mm ).
Since Sony A99's has a larger sensor area with the same resolution, this means that it also has a larger pixel area hence better light collecting capacity for a given aperture compared to Fujifilm X-Pro2.
Another difference between these two cameras is that Fujifilm X-Pro2'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 X-Pro2 and A99 sensor size comparison.
As seen above, Sony A99 has a 2.3x Larger sensor area than Fujifilm X-Pro2. 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.