The player underwent a medical in London on Sunday and both clubs had reached an agreement over a fee, however the deal has been called off after results of a second medical on Wednesday "prevented a contract between the player and Tottenham Hotspur from being concluded to the original conditions".
"The Brazilian national team player Gilberto will fulfil his contract until June 2008 with Hertha Berlin," announced the Bundesliga side on their website.
Meanwhile, Hertha claim they have found Tottenham's attitude "incomprehensible".
The German club now risk losing the player in the summer on a free transfer after a fee in excess of 10million euros had reportedly been agreed between the two clubs last week.
"Hertha BSC and Tottenham Hotspur reached an agreement over the transfer of the player after the statutory medical last Sunday, when all conditions for a transfer were fulfilled," added a Berlin statement.
"Which is why it is all the more incomprehensible for Hertha the way Tottenham have now acted."