Zabriskie moved to second place overall behind Belgium's Philippe Gilbert, who took the lead Tuesday.
The Team CSC rider clocked 52 minutes, 48.65 seconds for the 26-mile third stage that began and ended in Bourg-de-Peage.
Floyd Landis - winner of three races this year, including the Tour de Georgia in April - placed second, 53 seconds off Zabriskie's pace. Former Salt Lake City resident Levi Leipheimer was third, and Discovery Channel's George Hincapie placed fourth.
Today's stage is a 116-mile ride starting in Tain-L'Hermitage and finishing in Le Mont Ventoux. It's a climb.
"I'll try to do as well as I can," Zabriskie told cyclingnews.com. "I've never done the Ventoux before. Climbing gets hard for me when little Spanish guys go crazy."
The Dauphine Libere finishes Sunday in Grenoble. It's considered a warm-up for the Tour de France, which starts July 1.
