Goals from Christian Gentner and Vedad Ibisevic gave Stuttgart a 2-0 lead before Ivan Santini cut the deficit for the visitors in the 88th minute and set up a nervous finale as Freiburg desperately tried to get an equaliser.
Stuttgart beat Freiburg by the same score on Wednesday to clinch a spot in the German Cup final where they will face Bayern Munich.
Sunday's win lifted Stuttgart, who also hit the woodwork with Ibrahima Traore four minutes before the end, to 10th place on 39 points with four games left in the campaign.
For Bundesliga minnows Freiburg, who have been sparkling throughout the campaign, it was a bitter defeat after three straight wins, leaving them in fifth place on 45 points, one behind Schalke 04 and the spot that leads to the Champions League qualifiers.
In Sunday's later game, bottom club Greuther Fuerth gave themselves a slight chance of avoiding relegation with a surprise 1-0 win at FC Nuremberg.
Teenage midfielder Johannes Geis scored the only goal of the game on 27 minutes. His side are bottom of the 18-team division with 18 points, nine short of third-bottom Augsburg in the play-off spot.
- Sports & Recreation
- Ivan Santini