Daniel Caligiuri converted a penalty in the 40th minute for Freiburg's first goal and Julian Schuster doubled their advantage, and made sure of the points, with six minutes to go.
The result meant Wolfsburg remain bottom of the Bundesliga after suffering their fourth successive loss.
The hosts had the first chance of the game but Freiburg keeper Oliver Baumann held Ferhan Hasani's header on the line in the 18th minute.
Freiburg went close two minutes later but Wolfsburg keeper Diego Benaglio's reaction save stopped Jonathan Schmid's attempt.
Wolfsburg had a chance after 26 minutes but Ivica Olic's shot sailed just wide.
And it was Freiburg who went ahead after 40 minutes from the spot as Caligiuri converted the penalty after Naldo brought down Erik Jendrisek in the box.
Benaglio made another superb reaction stop to keep his team in the game three minutes after the re-start, denying the impressive Caligiuri.
Freiburg nearly made it 2-0 once more in the 63rd minute as Schmid's powerful effort crashed against the bar but bounced to safety.
The visitors were dominating and the woodwork denied Caligiuri once again two minutes later.
But Freiburg got the second goal their display deserved late on as Schmid picked out Schuster and he fired home from 15 yards to deepen Wolfsburg's troubles.