Born in Potsdam, Ebert started playing football for TuS Gaarden in Kiel as a four-year old in 1991. After two years he switched to TSV Russee in 1993, before his return to Berlin when joining Hertha BSC in 1998. From the 2006–07 season on, Ebert was part of Hertha's first team. He made his debut on 16 July 2006 in the Intertoto Cup against FK Moscow, coming on as a substitute in the 80th minute.
Ebert made his Bundesliga debut about a month later on 13 August 2006 against VfL Wolfsburg, scoring his first goal in the following match against Hannover 96. Since then, he has appeared in over 90 Bundesliga and 2nd Bundesliga matches for Hertha BSC.