Canon 90D has a 33.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 8 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.
Canon 90D's sensor provides 9MP 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 90D and A99 sensor size comparison.
As seen above, Sony A99 has a 2.6x Larger sensor area than Canon 90D. 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.