A header by midfielder Youssef El-Arabi five minutes from time silenced the Velodrome stadium and gave the visitors from Normandy a stunning victory.
Marseille, who secured their first league crown since 1992 last May, looked nervous throughout the match but seemed to have escaped with a draw after a late equaliser from substitute forward Mamadou Samassa until El-Arabi struck.
Caen deservedly opened the scoring when Marseille goalkeeper Steve Mandanda failed to parry a seemingly harmless angled effort from midfielder Nicolas Seube early in the second half.
Marseille coach Didier Deschamps was not pleased and made it clear the club, very quiet so far on the transfer market, needed to purchase new players.
"Caen were very determined and deserved to win but we showed many weaknesses," Deschamps told reporters.
"We made errors and lacked determination," he added. "We were the favourites and should have won that match. Now we know we need reinforcements if we want to be competitive."
SUPERB VOLLEYS
Last season's runners-up Olympique Lyon also struggled, managing only a 0-0 home draw with Monaco, although they did step up a gear after the break and created several chances.
Superb volleys from Paris Saint-Germain's Benin midfielder Stephane Sessegnon and newcomer Nene helped secure a 3-1 home win over St Etienne that made the Parisians early leaders.
"We need to do more than that in the future and we had a few problems at the back but it's encouraging," said PSG coach Antoine Kombouare, who struggled last season with frustrating results against a backdrop of violence from their unruly fans.
Some PSG supporters threw flares and briefly clashed with police outside Parc des Princes before kickoff to protest against a plan by the club preventing supporters choosing their seats. No injuries or arrests were immediately reported.
Toulouse might have to pay a heavy price for a 2-0 win over promoted Brest that put them second in the standings, with France striker Andre-Pierre Gignac leaving the pitch on a stretcher after twisting his ankle in the second half.
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