Both Nikon D5300 and Sony A99 have 24.0 MP resolution sensors but Nikon D5300'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 Nikon D5300.
Another difference between these two cameras is that Nikon D5300'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 D5300 and A99 sensor size comparison.
As seen above, Sony A99 has a 2.3x Larger sensor area than Nikon D5300. 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. Nikon D5300 and Sony A99 sensors have been tested by DxO and the results show that A99 has a better overall score of 89, 6 points higher compared to D5300's score of 83.