The 33-year-old former Team Sky rider who is returning from Epstein Barr virus, was not one of those injured in the gruelling racing conditions.
"Cavendish was forced to stop on the back of a challenging two days," his sports director Rolf Aldag said several hours after the race won by the the day before man tipped to become this season's dominant sprinter, Dutchman Dylan Groenewegen.
Former Team Sky rider Cavendish has not commented on his withdrawal.
"The race was just his third back," Aldag explained.
"As he continues to work his way back towards full fitness following a long lay-off from racing due to illness last year."
Tour de France contender Romain Bardet said the crosswinds had caused: "One of the top three hardest day's of cycling in my life."
Cavendish, known as the Manx Missile, and who specialises in pure sprint finishes, has won 30 Tour de France stages and harbours the ambition of overhauling Eddie Merckx's record of 34, said recently he felt he was still the fastest sprinter around.
He has had a glittering career, winning the road race world championships in 2011, a total of 48 Grand Tour stage wins, the Milan-San Remo classic and three track world titles and an Olympic silver medal at the 2016 Rio Games.