Porte, winner of this race in 2013 and 2015, finished the stage 14 minutes down after another wet, wild and windy day reminiscent of a Belgian classic than a race to the sun.
He lost contact with the lead group during a brutal first 50km of the 195km stage from Rochefort-en-Yvelines to Amilly which was blasted by crosswinds, his chances for a third Paris-Nice victory gone for good.
Orica-Scott’s Simon Yates was also a casualty of the difficult racing conditions.
Alberto Contador (Trek-Segafredo) also struggled for position over the first 50km but after a 100km chase his group rejoined the leaders and the Trek-Segafredo rider finished to fight on for the title.
Porte's demise was the second by a favourite in as many days after Romain Bardet (AG2R) was disqualified on Stage 1 for holding onto his team support car.
Colbrelli (Bahrain Merida) edged out John Degenkolb (Trek-Segafredo) and Arnaud Demare (FDJ) in the sprint finish after firing up his sprint with about 200 metres to go, to claim the biggest win of his career by half-a-bike length.
"I launched the sprint from far and it worked,” Colbrelli said. “I’m really happy because it's my first win in a race at such a level. It gives me a lot of confidence before Milan-San Remo, which is an important race for me after finishing 6th and 9th in the past."
Demare, who won the opening stage, remains in the overall lead, six seconds ahead of Quick-Step Floors’s Julian Alaphilippe and Philippe Gilbert, third at a further 11 seconds. Contador, is 1min 18sec behind Demare.
The third stage is again mainly flat and there is more rain and wind expected along the 190km route from Chablis to Chalon-sur-Saon.