The Belgian 2012 road race world champion has been suffering from an upper respiratory infection, which wasn't been helped by the cold, wet conditions on the opening three days of the French stage race. He did not start Wednesday's stage three.
"Phil’s condition is nothing to be overly concerned about, however the cold weather and snow that we saw in the opening prologue and first two stages of the race have done nothing but aggravate his condition,” said BMC Racing team medic Dr Dario Spinelli.
The 33-year-old will now focus on recuperating ahead of his main early-season target: Milan-San Remo on March 19.
“I really love this race so it is disappointing to have to stop racing," Gilbert said in a BMC statement. "But I have one of my biggest goals for the season, Milan-San Remo, around the corner and in order to perform well there I need to fully recover from this illness and be in the best shape possible."
Watch: Paris-Nice 2016 stage two highlights
Gilbert was sat in 104th place after stage two, won by overall leader Michael Matthews (Orica-GreenEdge).
BMC's highest-placed rider in GC is defending champion Richie Porte, who will be looking to make his mark during Wednesday's stage with its testing uphill finish.
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