The Quick-Step Alpha Vinyl leader had been targeting victory at the Ardennes Monument but was among the group of riders caught in a mass crash with 60 kilometres remaining.
A touch of wheels on the descent before the Col du Rosier sent Alaphilippe off-road and into a ditch at high speed, where he was quickly found by his concerned compatriot, Romain Bardet.
"It was just a nightmare," the DSM rider told VeloNews after the race.
"Tom Pidcock and a rider from Direct Energies crashed in front of me on the right, and I crashed on the right too, but I was really OK.
"When I looked around I saw Julian maybe five or six metres down, and it was an emotional shock because he was in a bad situation.
"No one was coming and he really needed help. It was an emergency situation. He couldn't move, he couldn't breathe."
Bardet's decision to climb down to Alaphilippe, and not back to his bike, allowed his rival to receive the necessary medical attention in an ambulance before being transported to a hospital in Herentals.
Quick-Step later confirmed the extent of the 29-year-old's injuries, along with teammate Ilan van Wilder who broke his jaw in the pile-up.
It was a bittersweet end to the Belgian team's classics campaign, who had Remco Evenepoel to thank after his 30-kilometre burst sealed a solo victory to remember.
The 22-year-old attacked at the top of the Cote de la Redoute and held firm to become the first rider to win the race on home soil since 2011, with Quinten Hermans (Intermarche-Wanty-Gobert) finishing second, and Wout van Aert (Jumbo-Visma) nabbing third.
