Wilson played in 40 games this season for Atlanta, serving as the backup shortstop. He hit .169 with a .189 on-base percentage.
General manager Frank Wren said as the front office evaluated the team going into September, it didn't see how Wilson fit in with the team.
"As we talked, we didn't see a definitive role," Wren said. "It's hard in September when you don't see that role."
Paul Janish has filled in capably as the starting shortstop for the last six weeks, replacing injured rookie Andrelton Simmons, who is expected to return in mid-September. Martin Prado and Tyler Pastornicky, who started at shortstop on Opening Day, are options as well.
Manager Fredi Gonzalez said Wilson took the news of his release well.
"He was fine," Gonzalez said. "He's a pro."
Wilson's release comes on the one-year anniversary of the trade with the Mariners to acquire him last year. In 57 games spread out over two seasons, Wilson hit .188 while providing backup at shortstop, third base and second base.