Omega Pharma-QuickStep rider Chavanel emerged from the slipstream of BMC’s Philippe Gilbert to snatch victory in Nice following the longest stage of this year’s race, a 220km run from Manosque.
Movistar’s Jose Joaquin Rojas was third in the bunch sprint ahead of Samuel Dumoulin (AG2R), Tony Gallopin (RadioShack), Julien Simon (Sojasun) and Borut Bozic (Astana).
Garmin’s American rider Andrew Talansky remains behind Team Sky's stage five winner Porte on GC, with Chavanel’s bonus seconds putting him third at 42s.
"I am super happy," said Chavanel. "It's the second time I won here in Nice, after my victory in 2008. It's always a great emotion to raise the arms here.
"Today I decided to do the sprint because I was looking for some points for the green jersey. There was a headwind in the final, so I asked Kevin De Weert to stay near me. He did a great job and he left me in the perfect position on the wheel of Gilbert and Dumoulin."
Eleven riders broke away on a soaking wet first half of the stage: Simon Clarke (GreenEdge), Egor Silin (Astana), Gatis Smukulis (Katusha), Eduard Vorganov (Katusha), Brent Bookwalter (BMC), Julien El Fares (Sojasun), Bozic, Jerome Pineau (Omega Pharma QuickStep), Romain Bardet (AG2R La Mondiale), Johann Tschopp (IAM Cycling) and Arnold Jeannesson (FDJ).
The latter rider stood 20th on GC - 1:49 in arrears of yellow jersey Porte – prior to the stage and so with the gap at 3:30 at the halfway point, he had the virtual lead for much of the stage.
With 86km remaining Latvian Smukulis was dropped by the leaders, while behind them the peloton picked up the pace to close the gap to 2:20 and drop Mark Renshaw and David Millar.
Renshaw’s subsequent abandonment left Blanco with five riders while FDJ were down to four after Yoann Offredo quit; Robert Gesink, Andreas Klier and Thomas De Gendt also called it a day on the stage.
The penultimate stage featured five categorised climbs, the last of them successive Cat.1s before a long run down into Nice.
Tschopp maintained his position in the break to lead them over both the Cote de Cabris and Col du Ferrier and put the seal on an impressive King of the Mountains triumph which raises hopes that IAM Cycling can secure a Tour de France wildcard spot.
After the climbs the gap was down to a minute; they had proven too much for El Fares, Silin, Bookwalter, Pineau and Bozic as the break was reduced to just five riders.
The peloton led by Sky and Euskaltel gradually ate up the remaining riders – Clarke, Vorganov, Bardet, Tschopp and Jeannesson (FDJ) – on the slippery descent.
Chavanel, Peter Velits (OPQS) and Andriy Grivko (Astana) attacked with less than 35km remaining but were quickly swallowed back up.
With the roads drying in the sun and Sky at the head of a strung-out peloton, Talansky stayed with Porte but was unable to break away from him.
The opportunity was there for an unlikely winner, with many specialist sprinters not in the running after the tough stage.
AG2R took to the front inside the final 2km then BMC came through, while Michael Albasini (Greenedge) was worked into position out wide with 500m to go.
He faded and it looked to be between Gilbert and the following Dumoulin, only for Chavanel to come through.
The race ends with a 9.6km individual time trial up the Col d'Eze which overlooks Nice.