Lampre sprinter Danielle Bennati (Lampre) took second-place in front of compatriot Luca Poalini (Liquigas) to make it an Italian one-two-three.
After Frenchman Thomas Voeckler (Bouygues Telecom), the only remnant of a four-man break-away, was caught in the final kilometre by a motoring Quick Step train, Pellizotti propelled through the ensuing confusion to victory.
Voeckler, Murilo Fischer, Stéphane Augé, and Philippe Gilbert attacked 50 kilometres into the 177-km stage from Vatan to Limoges.
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The peloton, led by Saunier Duval, Lampre and Quick Step, slowly closed the gap on the escapees until Augé and Gilbert were caught in the last 15-km.
Voeckler and Liquigas' Fischer made a courageous effort to hold off the peloton, which was led by a Quick Step team attempting to make up for a disappointing stage-one performance by sprinter Tom Boonen, but after the Frenchman tried a stunted attack, the two men slowed to a crawl just three kilometres from the finish line.
After dropping his break-away comrade, Voeckler made another dig at the solo victory, but was overtaken by a main group of sprinters in the final kilometre.
"With Fischer in the break, the Liquigas team did not have to work until the finale, Pellizotti told reporters.
"Near the finish, I sensed that Quick Step were very strong and were preparing the sprint for (Tom) Boonen. I found a way to sneak away in the last few hundred metres. I'm very glad to have won."
As the sprint teams tried to jockey for position at the front, Pellizotti saw his chance and took it, powering away from the main group in the final 100 metres.
Bennati put in a strong effort to catch his compatriot, but came up well short finishing two seconds behind the Liquigas rider.
Boonen's Quick Step train collapsed in the last 500 metres and the Belgian failed to even finish in the top-ten.
Voeckler, meanwhile, ultimately held onto tenth place.
Pellizotti takes over the general classification from previous leader David Millar (Saunier Duval) of Britain. Bennati is now third in the overall standings.
"The season is going very well for us. I think we've won four races so far," Pellizotti said.
"Personally, I badly wanted to do something on this Paris-Nice. Two years ago, I came second on a stage and I really wanted to win one. With the yellow jersey on top of it, the joy is complete."
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