Loewer attended Mississippi State University, and in 1994 he played collegiate summer baseball with the Hyannis Mets of the Cape Cod Baseball League. He was selected by the Phillies in the first round of the 1994 MLB Draft. Projected by Baseball America to be the 15th pick, he fell to the Phillies at 23rd overall primarily due to coming off an unimpressive junior season with the Bulldogs in which he had a 4.63 earned run average (ERA) and allowed 110 hits in 103 innings. He was ranked a top ten prospect in the Phillies organization by Baseball America for four straight years, reaching as high as fourth in 1995. While with the Scranton/Wilkes-Barre Red Barons in 1997, he established a franchise record for most strikeouts in a season with 152 which was surpassed by Matt Krook in 2022.
His MLB debut was a complete-game, five-hit 4–2 win over the Chicago Cubs at Veterans Stadium on June 14, 1998. He ended his rookie campaign at 7–8 with a 6.09 ERA. He pitched his first-ever major-league shutout in a 3–0 home victory over the Padres on May 4, 1999. He would not win another game until June 2, 2003 when he was with the Padres in a 4–1 triumph over the Arizona Diamondbacks at Qualcomm Stadium.
After a season in which he started 13 of 20 games and had a 2–6 record with a 5.12 ERA despite missing nearly four months because of a stress fracture in his right humerus, Loewer was traded along with Adam Eaton and Steve Montgomery from the Phillies to the Padres for Andy Ashby on November 10, 1999. The Padres' expectation for Loewer to become the third starter in its rotation was dashed two months after the trade when he suffered a compound fracture of his left tibia and a dislocated ankle as a result of falling out of a hunting blind in a tree near his home at the time in Eunice, Louisiana on January 2, 2000. He missed the entire season when he underwent surgery on July 18, 2000 to repair a partial rotator cuff tear which he sustained while recovering from his hunting accident injuries.

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