Both Pentax K-3 II and Sony A99 have 24.0 MP resolution sensors but Pentax K-3 II's sensor is APS-C (23.5 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 Pentax K-3 II.
Another difference between these two cameras is that Pentax K-3 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 K-3 II and A99 sensor size comparison.
As seen above, Sony A99 has a 2.3x Larger sensor area than Pentax K-3 II. 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.
DxOMark Sensor Scores
DxOMark is a benchmark that scientifically assesses image quality of camera sensors. It 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. Pentax K-3 II and Sony A99 sensors have been tested by DxO and the results show that A99 has a better overall score of 89, 9 points higher compared to K-3 II's score of 80.