Sejad Salihovic replied with a penalty for the hosts, still smarting from last week's 7-1 humiliation at Bayern Munich, but it was not enough as they continued a disappointing start for new coach Markus Babbel.
Hoffenheim have won once in six Bundesliga outings since Babbel replaced Holger Stanislawski in February and have dropped to 12th in the table with 30 points, seven clear of the relegation playoff spot.
"I think we were too naive over the 90 minutes although we played much better in the second half," said Babbel.
"That was too easy," said Babbel as he analysed a replay of the goal for German television.
The same combination set up Stuttgart's second goal two minutes before half-time as the Dutchman produced a low cross from the right and Ibisevic got in between two defenders to score with a diving header, his ninth league goal of the season.
