The Czech headed in a corner three minutes from time after Fortuna keeper Fabian Giefer's unsuccessful attempt to clear.
It was by no means a one-sided affair and Fortuna, who dropped to 15th, missed a golden opportunity of their own in the 80th minute but Andreas Lambertz' shot was saved by keeper Oliver Baumann.
Freiburg's Max Kruse hit the post in the dying seconds as the hosts confirmed their good form this season. Freiburg have also lost just one of their last seven games.
The result lifted them to 31 points, level with sixth-placed Mainz who stumbled to a 1-1 draw at relegation-threatened Augsburg, without a loss in the last five games.
Bayern Munich are cruising towards their first Bundesliga title since 2010 after crushing Schalke 4-0 on Saturday to open up a 15-point lead over champions Borussia Dortmund, who suffered a 4-1 home loss to Hamburg and have 39 points.
Bayer Leverkusen stayed in third place on 38 after conceding a late equaliser in their 3-3 draw at Borussia Moenchengladbach.