Vedad Ibisevic put the visitors ahead in the ninth minute and Timo Werner doubled the lead just 60 seconds later.
Second-half substitute Mike Hanke pulled one back for Freiburg in the 78th minute almost immediately after being introduced as a substitute, but Werner netted his second of the match four minutes later as Stuttgart climbed to eighth in the table.
Freiburg, by contrast, remain 16th with just one win from 12 league outings.
Elsewhere, Mainz climbed to ninth with a 1-0 home win over Eintracht Frankfurt.
Maxim Choupo-Moting, who came off the bench in the second half, struck an 88th-minute winner to clinch a second victory in three games for his side.
Frankfurt have now suffered four successive defeats in all competitions and are winless in seven Bundesliga matches.
