The three points moves former league leaders Hertha up from fourth to second in the table and two points behind Wolfsburg who are in action on Sunday at struggling Cottbus.
But fellow former league leaders Hoffenheim are now virtually out of the title race as they suffered their third defeat in their last four games and are now down to eighth in the league, 12 points behind Wolfsburg.
This was Ebert's first goal for Hertha since being demoted to the reserves and fined last month after being questioned by Berlin police when his 22nd birthday celebrations got out of hand and several cars were vandalised.
The winning goal came when Berlin striker Marko Pantelic turned provider by sliding his pass through the Hoffenheim defence and Ebert rolled his shot past diving home goalkeeper Timo Hildebrand on 40 minutes.
This was Berlin's second consecutive league win following last weekend's victory over Bremen, but either Bayern Munich or Hamburg can reclaim second spot depending on Saturday's results.
Hamburg are at mid-table Dortmnd on Saturday while Bayern host sixth-placed Schalke who are chasing a place in Europe for next season.