The former Tampa Bay Rays player, assistant and coach will be a first-time manager, the first in the major leagues born in the 1980s.
The only year as a professional he spent apart from the Rays was 2009, when he played in 62 games for Boston.
The team's previous manager, Paul Molitor, was sacked in early October after the Twins finished with a disappointing 78-84 record.
Baldelli has declined comment throughout the managerial search process, having also interviewed with the Blue Jays and Rangers, who still were interested, and the Angels and Reds, who hired others.
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While it's not news that the Twins were in the market for a new skipper after firing Paul Molitor, the Internet was shook when it realized that Baldelli is only 37 years old.
Molitor was named the American League Manager of the Year in 2017.
The Twins need someone who can reach young players, as Byron Buxton and Miguel Sano in particular have faded from highly touted prospects to disappointing major leaguers.
As it turns out, the Twins were looking for a younger manager that could communicate well with millenials.
"He is beyond a wonderful representative of the Twins - he is the Twins in a lot of ways", Baldelli said, . He joined the Padres after spending three seasons as the Dodgers' hitting coach.