The Australian striker pounced on a deflected shot to tuck home in the 12th minute before doubling his side's lead eight minutes before half-time with a first-time effort from the edge of the area.
Stuttgart replied through Christian Gentner on the hour-mark before Kruse's teammate Oliver Fink wrapped up proceddings with just under 15 minutes remaining and the former Melbourne Victory star was thrilled with both his individual and the team's performance.
''Personally, it is always great to score two goals, but it was far more important to get the three points,'' Kruse told AFP.
''We worked together really well today and had an excellent structure in our game. We were very disappointed after the last two defeats, but we worked really hard in training last week and our reward was a great performance I'm much happier about the team's success than about my two goals.''
Kruse has now scored four goals in 18 outings for Fortuna this season with the club sitting 13th on the Bundesliga table.