Freiburg _ with its fifth home win in six matches _ climbs back up to fifth place with 26 points, one above defending champion Bayern Munich, while Moenchengladbach remains bottom.
Cisse opened the scoring in the 19th minute when he got between two defenders to meet a perfect cross from Maximilian Nicu with a powerful header.
Oliver Barth made it 2-0. Barth, a defender, was first to react when goalkeeper Christopher Heimeroth was unable to hold onto a powerful shot from Cisse.
The Senegalese completed the scoring when he was left unmarked to meet a free kick from Julian Schuster with a simple tap in.