Along with outfielder Carlos Gómez and pitchers Philip Humber and Kevin Mulvey, Guerra was traded to the Minnesota Twins for Johan Santana on January 29, 2008.

With the Fort Myers Miracle, he compiled a 7–2 record with a 4.83 earned run average in the first half of the 2008 season—helping his team capture the Florida State League (FSL) first-half West Division title.
Guerra's first start in the second half of the 2008 season (Tuesday, July 1) was a 4–0 complete game shutout of the Tampa Yankees.
He allowed only three hits, and retired 19 in a row between a first inning single by James Cooper and a one-out single by Andres Perez in the seventh.
It marked the first shutout of Guerra’ professional career.
For the second half, he went 4–7 with a 6.08 ERA in 13 starts.

The Miracle again captured the first half division title in 2009, this time in the FSL's newly realigned Southern Division, and Guerra brought a no hitter into the eighth inning of a July 3 game against the Charlotte Stone Crabs.
With one out, Christian López broke it up with a double down the left field line.
Guerra was promoted to the New Britain Rock Cats immediately after this game (July 7).
 He was named FSL pitcher of the week for the week of June 29 through July 5.
His combined record for Fort Myers and New Britain was 12–11 with a 4.89 ERA and 106 strikeouts.

On November 20, 2009, he was added to the Twins' 40-man roster.
He began the 2010 season with New Britain, going 1–1 with a 3.07 ERA in five starts prior to being promoted to triple-A. During the 2012 season, the Twins converted Guerra into a relief pitcher.
The Twins removed Guerra from their 40-man roster after the 2012 season.

Guerra competed for the Venezuelan national baseball team in the 2013 World Baseball Classic.
He was hospitalized with a blood clot in his right shoulder in March 2013.
Along with outfielder Carlos Gómez and pitchers Philip Humber and Kevin Mulvey, Guerra was traded to the Minnesota Twins for Johan Santana on January 29, 2008.
With the Fort Myers Miracle, he compiled a 7–2 record with a 4.83 earned run average in the first half of the 2008 season—helping his team capture the Florida State League (FSL) first-half West Division title. Guerra's first start in the second half of the 2008 season (Tuesday, July 1) was a 4–0 complete game shutout of the Tampa Yankees. He allowed only three hits, and retired 19 in a row between a first inning single by James Cooper and a one-out single by Andres Perez in the seventh. It marked the first shutout of Guerra’ professional career. For the second half, he went 4–7 with a 6.08 ERA in 13 starts.
The Miracle again captured the first half division title in 2009, this time in the FSL's newly realigned Southern Division, and Guerra brought a no hitter into the eighth inning of a July 3 game against the Charlotte Stone Crabs. With one out, Christian López broke it up with a double down the left field line. Guerra was promoted to the New Britain Rock Cats immediately after this game (July 7).  He was named FSL pitcher of the week for the week of June 29 through July 5. His combined record for Fort Myers and New Britain was 12–11 with a 4.89 ERA and 106 strikeouts.
On November 20, 2009, he was added to the Twins' 40-man roster. He began the 2010 season with New Britain, going 1–1 with a 3.07 ERA in five starts prior to being promoted to triple-A. During the 2012 season, the Twins converted Guerra into a relief pitcher. The Twins removed Guerra from their 40-man roster after the 2012 season.
Guerra competed for the Venezuelan national baseball team in the 2013 World Baseball Classic. He was hospitalized with a blood clot in his right shoulder in March 2013.
Deolis Guerra