Used baseballs are either thoroughly cleansed to be used in other games, used in batting practice, or recycled to make new baseballs.
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They use them for batting practice or give them away to fans at the game. Most balls only last 3-5 pitches. The teams may go through 60 or more baseballs in a game.
Usually MLB balls are fouled off into the stands. But the one that is used to record the final out is given to someone on the club to auction off.