It was the first super-G race win for Rebensburg, whose other six career World Cup wins are all in giant slalom. She was clocked in 1 minute 24.54 seconds, putting up what proved to be the winning time in an early run and then waiting out the rest of the field.
American skier Julie Mancuso was second at 1:24.72 and France's Marion Rolland took third in 1:24.75.
Vonn finished sixth at 1:25.11 but still collected her 16th discipline championship and fourth consecutive super-G title. Vonn has also claimed the 2011-12 overall, combined and downhill titles.
She is second in the giant slalom with one of two events still to be decided this season. Rebensburg leads the giant slalom standings with 550 points, 95 more than Vonn.
Vonn said this week she was shooting for the overall point total record of 2,000 by Hermann Maier. She is at 1,948 after Thursday's results.