I can't tell you how sad I am, there's really no words. The Tour de France was my primary goal of the year, and to miss it, after previously being forced to skip the Ardennes Classic, it's very disappointing," the 24-year-old, who underwent surgery on Wednesday, said in a team statement.
"Now my focus is on making a full recovery and arriving in a good condition for the second part of the year. Fortunately, the season is still long and I hope to bounce back."
Alaphilippe won the Tour of California last year and finished fourth in the Olympic road race in Rio de Janeiro.
This year, he finished fifth overall in the week-long Paris-Nice race and third in the Milan-San Remo classic.
The Tour de France starts on July 1 in Duesseldorf, Germany. SBS will broadcast and stream every stage live from start to finish.