Freire, wearing the world champion's jersey, finished the sprint just ahead of Australia's Robbie McEwen and Germany's Zabel.
Bertogliati kept the yellow jersey as the overall leader and is two seconds ahead of Zabel.
Zabel, the Telekom team's top rider with the absence of American Lance Armstrong's great rival, Jan Ullrich, finished second in Sunday's stage and is gunning to win the green jersey as the Tour's best sprinter for an unprecedented seventh time.
Armstrong, the three-time defending Tour champion and winner of Saturday's prologue, dropped one spot Monday to fourth, just behind Frenchman Laurent Jalabert.
The Texan is looking to stay within striking distance of the leaders until the mountain stages begin on the 10th leg July 17. Armstrong effectively won the 2001 title with his climbing prowess.
Armstrong is attempting to join Frenchmen Jacques Anquetil and Bernard Hinault, Belgian Eddie Merckx and Spaniard Miguel Indurain as the only cyclists to win the race more than three times.
Bertogliati, a rider for the Lampre Daikin team, shocked the pack Sunday when he started a solo sprint for the line with just over a half-mile left in the 121.17-mile stage. It was the first career stage win for the 23-year-old.