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 05 who stumbled to a 1-1 draw at relegation-threatened Augsburg, without a loss in the last five games.
The visitors broke the deadlock just before the break, taking advantage of a lapse of concentration in the Augsburg defence after right back Ronny Philip was stretchered off and American Michael Parkhurst replaced him.
Adam Szalai was left unmarked, lurking at the far post when two defenders failed to clear a seemingly harmless cross and the Hungarian drilled in for the lead with his 12th league goal of the campaign.
Mainz, however, were left with 10 men minutes later when Shawn Parker was sent off for a rough challenge on Parkhurst and the hosts quickly made the extra man count when Sascha Moelders headed in from 10 metres to level in the 57th.
Augsburg are still 17th in the league but have now moved to within a point of Hoffenheim, in 16th.
Bayern Munich are cruising towards their first Bundesliga title since 2010 after crushing Schalke 04 4-0 on Saturday to open up a 15-point lead over champions Borussia Dortmund, who suffered a 4-1 home loss to Hamburg SV and have 39 points.
Bayer Leverkusen stayed in third place on 38 after conceding a late equaliser in their 3-3 draw at Borussia Monchengladbach.
