Bernucci finished the largely flat 123.7-mile stage from Troyes to Nancy in 4 hours, 12 minutes 52 seconds, not fast enough to take the yellow jersey from overall leader American Lance Armstrong.
The defending champion stuck with the pack, finishing 69th but scathed in the sixth stage.
Alexandre Vinokourov was 3 seconds behind Bernucci, good enough to move up to third place in the overall standings.
George Hincapie was second overall, still 55 seconds behind Armstrong, his Discovery Channel teammate. Vinokourov trailed Armstrong by 1 minute, 2 seconds and Jens Voigt was 2 seconds behind Vinokourov.
Christophe Mengin of France was leading before sliding out of control and creating a domino effect of falls that included Robbie McEwen, winner of Wednesday's fifth stage.
"Obviously it was a hairy finish," said Armstrong. "When you're stuck behind a crash like that you just have to sort of pick your way through and make it to the finish."
The 142-mile seventh stage begins Friday in Luneville, France, and ends in Karlsruhe, Germany.