The Australian fell in the Arras-Roubaix stage nine, before the race hit the first of 15 cobbled sectors. He dislocated his right shoulder and pulled out immediately.
The team is set to wind up this year, with Porte tipped to move to Trek Segafredo. He has perhaps one more chance, at this year's Vuelta a Espana, to win a Grand Tour for BMC.
"It was stage nine last year, too," said team-mate Stefan Küng. "Getting Richie on the podium in Paris in BMC colours just wasn't meant to be."
Porte crashed in the first half-hour after leaving Arras for the cobbled journey to the famous monument finish at Roubaix. He never had a chance to ride the cobbles that had caused so much consternation since the race began last Saturday.
"There was nothing he could have done differently," added Küng. "I was on the right hand side of the road and he was in the middle of it. At this point it just happened. I was a big bummer to the team."
Yellow jersey leader Greg Van Avermaet had the freedom to ride his own race even before the stage began, while the other six men aimed to stay with classification leader Porte.
With the Australian out, Van Avermaet took the focus. He made the lead group of three, but lost the day to John Degenkolb (Trek-Segafredo). He did however extend his yellow jersey lead to 43 seconds over Geraint Thomas (Team Sky).
Porte never had a chance to lead BMC to the top in Paris, unlike his compatriot Cadel Evans in 2011. Last year Porte crashed in stage nine and fractured his collarbone and pelvis.
"It was a pretty hectic day, we lost Richie after 10 kilometres," Van Avermaet said. "Two years in a row. You can lose one year your GC goal but now two years, at 32, it is not the best for him. It will not be easy to get back for him mentally. Good thing his crash was not as bad as last year."
"We have worked on this for a whole year," Allan Peiper, BMC Racing's performance manager said.
"This was a whole year of work from a big organisation. This is the pinnacle event, we have worked for that with Richie Porte and it is taken away from you in a flash.
"There is a lot of hope that a lot of people carry, and there is a lot of work that a lot of people have put in, and it's gone just like that."
Team boss Jim Ochowicz gave an update on Porte's situation and was already looking to the future.
"He seems to be OK," he said. "They transported him to Cambrai. We have a vehicle there and we got to pick him up. He will get down to Annecy tonight and probably go home tomorrow with his family [in Monaco].
"He's fine and now we make a new plan. What do we do? Maybe we are looking at the Vuelta a España now. That is not such a bad thing. He is in good form.
"He is going to go home and heal, but again it is not a fracture that is going to keep him out from training for six weeks. He will back on his bike in a couple of days."
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