The 2004 Russian champion refused to surrender in the finale when his three breakaway companions had to give up the fight and the Team-CSC rider managed to hold the bunch at bay until the finish line where he was 12 seconds clear.
Italian Franco Pellizotti, winner of the previous stage in Limoges, retained his overall lead with a two second edge over Italy's Daniele Bennati.
"It was a great day for me, first with the four-man break and of course because of the outcome. I really did not think I could make it to the finish," said Kolobnev.
Liquigas upstage Savoldelli's Astana
The Russian, 26, broken away after only 2.5 kms with three other riders, Italian Fabio Baldato, France's Nicolas Vogondy and Australian-born German Heinrich Haussler.
"In the final 15 kms I decided to go on my own and to take advantage of the long final descent." said Kolobnev.
Winner of five Paris-Nice stages in the last two years, Boonen was obviously back in great form in this longest stage in the Race to the Sun 2007.
He beat Italian Bennati in the main pack's sprint to take second place.
The 2005 world champion raised an arm as though he had won but the day belonged to a lesser-known Russian, who managed to stage the first successful breakaway in the race so far.
Boonen, who has already snatched seven wins this season, had won the first two Paris-Nice stages in 2005 and in 2006, but it will be hard for him to collect his first victory in Thursday's ride to Mende.
The 169.5-kms fourth stage is the hilliest on the menu this week, finishing with a first category climb.
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