In the overall standings, Peterhansel increased his lead to 27mins 33secs over Alphand and 1hr 30mins 55secs over Germany's Jutta Kleinschmidt, driving a Volkswagen.
Boisson, who has never finished on the podium at a World Cup event, claimed France's first medal in the sport's premier discipline since Luc Alphand also took bronze in 1996.