Commerzbank, which previously owned more than 82% of Comdirect, has been in the process of taking over the entire online bank as part of a broader restructuring.
Commerzbank bought the stake from Petrus Advisers, which said in December that it owned 7.5% in Comdirect. Commerzbank and Petrus had been in talks about the sale, a person said earlier this week.
A stake of 90% under German law allows Commerzbank to squeeze out remaining shareholders.
Martin Zielke, Commerzbank's chief executive, said the sale was an "important step to quickly and efficiently execute the integration of our successful direct banking subsidiary".
Petrus Advisers declined to comment.
(Reporting by Tom Sims and Hans Seidenstuecker; editing by Thomas Seythal and Thomas Escritt)