Flowers hit .195 with a career-high 10 homers and 24 RBIs in 84 games this year. He is a .200 hitter in 192 career games over five seasons with the White Sox.
The 27-year-old Flowers had season-ending right shoulder surgery on Sept. 5, but is expected to be ready for spring training.
Chicago also announced on Monday that it did not tender a 2014 contract to right-hander Dylan Axelrod, who went 4-11 with a 5.68 ERA in 30 games last season, including 20 starts.
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