Bauer was born in Los Angeles, California and is of Irish and German descent. He attended high school at Miramonte High School in Orinda, California and played on the Miramonte football team in his senior year, 1984, the year the team won the state championship. Later, he attended the University of San Diego, the American Academy of Dramatic Arts and graduated from the Yale School of Drama.

Bauer's first film appearance was in Snow White: A Tale of Terror, with Sigourney Weaver, Sam Neill, and Monica Keena. Soon after, Bauer played schoolteacher/pedophile Lloyd Gettys in the 1997 film The Devil's Advocate. He played prisoner NB9674932-65 Ivan Dubov in the 1998 action film Face/Off, where he met Nicolas Cage. He then appeared as the masked character 'Machine' in the 1999 film 8mm also starring Cage. He starred as fetish Photographer Irving Klaw in the 2005 Bettie Page biopic The Notorious Bettie Page, and as famous author Ken Kesey in a 2007 Neal Cassady biopic. Bauer played a small role in the 2005 Jim Jarmusch film, Broken Flowers. He was featured in the movie The Conspirator, as a fellow officer following Abraham Lincoln's assassination, and played a minor role in Flags of Our Fathers. In 2015, Bauer played the role of 'Pa' in Disney's Tomorrowland. He also appeared in "Money Monster" as Lt. Nelson, and played Larry Rooney in "Sully".

Bauer has starred in numerous television series including The Wire as port-union boss Frank Sobotka. He initially auditioned for the role of Jimmy McNulty. He also starred in Billy Crystal's 2001 film 61*, as New York Yankees player Bob Cerv. His roles on network television include a regular role as Fred Yokas, husband of Officer Faith Yokas, on the NBC series Third Watch, lead FBI Agent Dodd on the short-lived CBS series Smith, a Priest on ABC's Life on Mars and as Detective Lou Destefano in the original Sci-Fi channel miniseries The Lost Room. In 2004 he played 'Lee Nickel' on the ESPN series 'Tilt". He appears on the episode The No-Brainer of the television series Fringe as Brian Dempsey. He also appeared in multiple episodes of Numb3rs as Dr. Raymond "Ray" Galuski and in Criminal Minds in season one as the antagonist.

Chris Bauer played Det. (later Sheriff) Andy Bellefleur on the TV-series True Blood. He also played Dennis Halsey, a guard on Unforgettable in the fourth episode of the first season, "Up In Flames", and appeared as a rival salesman from the Syracuse branch of Dunder Mifflin in Season 8 of The Office (US). In 2014, Bauer guest starred in an episode of NBC's Parks and Recreation. In October 2014 Bauer started a recurring role on the Starz comedy Survivor's Remorse. He plays Jimmy Flaherty, the owner of a fictitious Atlanta professional basketball team. The show is written by Mike O'Malley, who is also an executive Producer along with NBA star LeBron James, and stars Jessie T. Usher. Survivor's Remorse started its second season on September 22, 2015. Bauer played Det. Tom Lange in the FX limited series American Crime Story. Bauer appeared as Tim Rutten in the NBC mini-series Law and Order True Crime: The Menendez Brothers, and from 2017 co-stars as Bobby Dwyer in the HBO series The Deuce.