Patrick Reusse of the Minneapolis Star-Tribune first reported the news.
Gardenhire had been the team's manager since 2002. He is the first manager to be fired by the organization since Ray Miller in 1986.
Gardenhire, who had one season remaining on his contract, said last week that he wanted to return for a 14th season. General manager Terry Ryan said Sunday he would meet with each coach individually before determining if they'd be brought back.
The Twins finished 70-92 this season, marking their fourth straight season of losing 92 or more games since last making the playoffs in 2010. Minnesota has finished in last place in the American League Central in three of those four seasons, including this year.
During his 13-year tenure as manager, Gardenhire led the Twins to six playoff appearances, all in his first nine years in charge of the club, and advanced as far as the ALCS in 2002, falling to the then-Anaheim Angels in five games.
The team hasn't won a playoff game since 2004. The 2002 ALDS was the only playoff series the Twins won under Gardenhire.
Minnesota went 1068-1039 with Gardenhire as manager and 6-21 in the postseason.
Gardenhire was named Manager of the Year in 2010 after leading the team to a 98-64 mark.
Before beginning his coaching career, Gardenhire spent five seasons with the New York Mets from 1981-85. He managed in the Twins' farm system from 1988-90 before becoming Minnesota's third base coach in 1991, a position he held until he was promoted to manager in 2002.
- Ben Estes