Van Aert and Alaphilippe were able to continue but Tadej Pogacar lost key teammate Tim Wellens while another fancied rider Britain's Tom Pidcock lost Ben Turner.
Former winner Peter Sagan also had to pull out of the race due to the fall.
The accident happened around 140km into the 273km cobbled-classic marathon as Bahrain Victorious rider Filip Maciejuk hit a pot hole whilst trying to get around the peloton on a verge of grass.
Maciejuk was expelled from the race within minutes.
"I'm really sorry for my mistake and causing the crash today," said the embarrassed Polish rider.
"I hope all those involved are in good health and safe. This should not happen and was a big error in my judgement."
He added: "All I can do now is apologise for my mistake and learn from this in the future."
French rider Valentin Madouas pulled out with a stomach issue.
