Voigt and Pereino dueled the final two kilometers but it was Voight winning the 230-kilometer stage 13 from Beziers to Montelimar in southern France in a time of five hours, 24 minutes and 36 seconds.
France's Sylvain Chavanel was third, Italy's Manuel Quinziato fourth and Andriy Grivko of Ukraine fifth, trailing the leader by more than six minutes.
Landis, who began the day wearing the yellow jersey of overall race leader, finished 29th and fell into second place overall, one minute 29 seconds behind Peneiro. Cyril Dessel was third overall eight seconds behind Landis.
Sunday's 14th stage of the Tour takes the racers on a 180.5-kilometer trek from Montelimar to Gap.