The drone flew above the training pitch several times on Tuesday as the players prepared for the game.
"The suspected pilot was located," Hoffenheim said. The club did not give any more details on whether the drone was used for recreational purposes or to spy on their training.
"The case was handed over to the police who have already launched an investigation," club spokesman Holger Kliem told reporters.
Hoffenheim, unbeaten in the last five matches against Werder, are eighth in the standings, two points ahead of their opponents.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
