St. Louis won the NL Central with a 91-71 record under Shildt after missing the playoffs the three prior seasons. Shildt owns a 132-99 record since taking over following the firing of Mike Matheny last year.
The news comes one day after the death of Shildt's mother Elizabeth.
Shildt won the honor despite garnering fewer first-place votes than Milwaukee Brewers manager Craig Counsell. It's the second time in MLB history a winner has received fewer first-place votes than the runner-up; Lou Piniella won in 1995 despite getting two fewer top votes than Kevin Kennedy.
Shildt is also the first MLB Manager of the Year winner to never play baseball at a professional level.
Twenty-seven of 30 writers named Shildt on their ballots. ESPN's Sam Miller of the Los Angeles chapter, The Associated Press' Will Graves of the Pittsburgh chapter, and MLB.com's Matthew Leach of the Atlanta chapter were the only holdouts.
Brian Snitker of the Atlanta Braves was looking to become the second back-to-back recipient of the award after Bobby Cox won in 2004 and 2005 while also leading the Braves.