Caen, who had started their campaign with a shock 2-1 win at Olympique Marseille, picked up three points again, this time against last season's runners-up. Midfielder Ismaila N'Diaye scored the winner with a fine volley on 77 minutes.
Visitors Lyon twice fought back from a goal down with two goals from forward Bafetimbi Gomis but were reduced to 10 men with a second booking for Anthony Reveillere just before half-time.
"We have lots of injury worries but that's no excuse," Lyon coach Claude Puel, who was already missing Argentine striker Lisandro Lopez, told reporters. "We must raise the level of our game and we must do it fast."
"Losing your first match can happen, especially when it's an away game, but losing the first two is a nuisance," Bordeaux president Jean-Louis Triaud told reporters. "What I didn't like was that we were not aggressive enough."
