When pitching, a box with a blue circle inside will appear. Within the center of the circle is a red dot. A ring will move inside and out the box. Try to time your pitch so that the ring is exactly center on the red dot to throw a perfect pitch. This will be the fastest pitch, making it difficult to hit. You can also move the blue circle around with the left joystick to angle the ball in a different direction. Do not throw the ball too far from the batter.
You can opt to instantly throw a perfect pitch without manual input by selecting the "Perfect Pitch" option. This will cost a large portion of your pitcher's stamina.