Beimel was originally drafted during his first year of college on June 4, 1996 by the Texas Rangers, but declined to sign, to stay in school. Following his junior year he was drafted again, this time signing with the Pittsburgh Pirates on June 2, 1998. Beimel joined the Pirates' minor league affiliates the same year, where he stayed for his first few seasons.

On April 8, 2001, Beimel was called up to make his MLB debut with the Pirates. He split his first season and the following two between the Pirates and the minors. Days before the start of the 2004 season, Beimel was released by the Pirates.

Beimel signed as a free agent with the Minnesota Twins on April 11, 2004. He played only three games with the Twins, allowing eight hits in less than two innings and finishing the season with a 43.20 earned runs average. Following the season, he was released by the Twins.

Beimel signed with the Tampa Bay Devil Rays on November 5, 2004. He spent the majority of his time in the minors, playing seven games with the Devil Rays during the 2005 season.

On January 24, 2006, Beimel signed with the Los Angeles Dodgers. He played 10 games with the Dodgers' minor league affiliates before earning a full roster spot during the 2006 season. He played 62 games with the Dodgers in 2006, finishing with a career best 2.96 ERA. He was however forced to the bullpen for the Dodgers post season run, after cutting his hand at a bar.

Beimel rejoined the Dodgers in 2007, playing a career high 83 games and finishing with a 3.88 ERA.