American Shiffrin, who has dominated the overall standings this season, skidded out on her first run in Kronplatz, Italy, surrendering the top spot of the giant slalom rankings to her German counterpart in the process.
Rebensburg edged out Norwegian Ragnhild Mowinckel by 0.03 seconds, winning in a combined 2:06.09.
Federica Brignone's 2:06.85 was good enough for bronze, giving the home crowd something to cheer, just ahead of compatriot Marta Bassino, who had to settle for fourth.
Swiss oust great rivals Austria to win inaugural Alpine team event gold
Rebensburg's winning Giant Slalom run at Kronplatz
After two victories to start the season, Rebensburg was back to winning ways after failing to make the podium in each of the last three giant slalom rounds.
Her 100 points sees her move on to 422 in the giant slalom World Cup standings, 37 ahead of Shiffrin on 385, with France's Tessa Worley third on 370.
However, Shiffrin remains dominant in the overall standings, with her total of 1477 more than double that of second-place Rebensburg (634) and Tina Weirather (601) in third.