TuS Mayen and Eintracht Trier Bauer grew up in
Andernach and began playing football at local club SC Concordia Saffig before progressing to
TuS Mayen, where he featured for both the youth and senior sides. In the
Verbandsliga Rheinland, then the fifth tier of German football, he won promotion to the
Oberliga Südwest in his first senior season; the club finished twelfth the following year before Bauer moved on. In 2002, described at the time as a goal-threatening talent, Bauer joined
Eintracht Trier—who were entering their first
2. Bundesliga season under coach
Paul Linz—and established himself as a
defensive midfielder. He made 26 second-division appearances across three seasons, during which Trier were relegated on the final day of the
2004–05 season on goal difference. Bauer remained at the club for the following
Regionalliga Süd campaign, adding ten appearances, but a managerial change midway through the season left him on the margins and eventually playing for the reserve side; he departed in the summer of 2006. He eventually signed for Union Berlin the following January and made ten
Regionalliga Nord appearances before the season ended, though the two parties could not agree terms on a new contract. After a further period without a club, Bauer signed for Finnish top-flight side
RoPS and made nine
Veikkausliiga appearances before fracturing his shoulder blade in June, ruling him out for the remainder of the season. A serious injury limited him to 16 appearances in his first full season, but he extended his contract in May 2010 until June 2011 and was made captain for the
2010–11 season. With the club struggling at the bottom of the Regionalliga in the
2011–12 season, Bauer had already reported written death threats to police two months before he was attacked, but said he was sent away without action being taken. On the night of 27 October 2011, several masked men wearing club colours entered his apartment building and threatened him verbally, demanding that the side win an upcoming derby against
Hallescher FC or face a return visit. Bauer later recalled that "six or seven men, all wearing Magdeburg balaclavas" had stood at his door: "A complete moment of shock." The club filed a criminal complaint, stripped Bauer of the captaincy, and listed him as absent from the derby "for personal reasons" without consulting him. Bauer fled to his hometown near
Koblenz and, after club president Peter Fechner publicly dismissed concerns about the incident, requested that his contract be dissolved by mutual consent. Charges were subsequently brought against one identified individual; investigators were unable to identify the remaining perpetrators. He made 64 appearances in total for the club, scoring five goals.
Later career Bauer rejoined
Eintracht Trier in January 2012, returning to the club where he had spent the first four years of his senior career. Now competing in the
Regionalliga Südwest, the fourth tier, he saw out the season before moving on that summer. Bauer signed with
VfB Oldenburg in summer 2012, who had just won promotion to the
Regionalliga Nord after a twelve-year absence from the fourth tier, joining alongside his brother Tobias Bauer. The arrangement collapsed in January 2013 when sporting director
Frank Neubarth announced that both Bauer brothers had been dropped from the squad, stating the club "had no other choice"; Daniel Bauer maintained the pair "had always conducted themselves impeccably". Bauer joined the
reserve side of
Hannover 96 for the remainder of the season and retired from playing at the end of 2013–14, aged 31. ==Managerial career==