Benes was born in Evansville, Indiana, where he attended Evansville Lutheran School and Evansville Central High School along with his brother Alan. He was the first player selected in the 1988 Major League Baseball draft after playing college baseball at the University of Evansville. Benes pitched well enough in his first year to make it to the majors and be named National League Rookie Pitcher of the Year by The Sporting News.
Benes was an All-Star in 1993 during a 15–15 season with the Padres, and led the Majors in losses with 14 and in strikeouts with 189 the next season. Benes finished third in the Cy Young Award balloting in 1996 after an 18–10, 3.83 earned run average season. After the 1997 season, Benes agreed to sign a 5-year, $30 million contract to return to the Cardinals. Unfortunately, the contract was signed after the deadline for players to re-sign with their 1997 teams. Benes would then have to wait until May 1 to re-sign. Instead, Benes became one of the first players in Diamondbacks history when he signed as a free agent prior to the 1998 season and threw the first pitch in the history of the franchise.
Benes was primarily a starting pitcher but on May 29, 1996, he picked up his only major league save. He recorded the final out of a 6–5 Cardinals victory over the Rockies to close out the game for the Cardinals.

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