Heading into the 293km monument, the team had three potential winners in its arsenal - world champion Michal Kwiatkowski, Strade Bianche winner Zdenek Stybar and 2009 San Remo winner Mark Cavendish.
However in the end no Etixx-Quick-Step rider contested the finale on Via Roma that was won by John Degenkolb (Giant-Alpecin) ahead of defending champion Alexander Kristoff (Katusha) and Australia's Michael Matthews (Orica-GreenEDGE).
Cavendish was the best-placed of the Etixx-Quick-Step riders, finishing 23 seconds down in 46th place.
"I didn't feel good at all, I had nowhere near the form I had a few weeks ago before I got sick," said Cavendish.
"But the team put me in good positions for the climbs. I kept fighting just for the chance to be there at the finish. A kilometer and half to go on Cipressa, when it was more flat, I had a mechanical. My chain went off. I used some energy I needed with my condition in order to close the gap on the descent.
"Then before the start the Poggio I was behind a rider who lost the wheel in front of him for a moment, and at Milano-Sanremo any gap at all can cost you the race. On the Poggio you have to keep moving up and fight for position, and I didn't have the energy to do the accelerations necessary at that point. The combination of how I felt and my energy expenditure catching back to the peloton after my mechanical just put me too far back."
While Cavendish was struggling, Kwiatkowski and Stybar remained in good positions heading into the descent of the Poggio. However an ill-timed crash saw the Etixx-Quick-Step pair, along with 2013 champion Gerald Ciolek (MTN-Qhubeka) and Philippe Gilbert (BMC), hit the deck which ruled them out of contention.
"Today I was really unlucky," Stybar said. "I crashed twice."
"The first time I crashed on the downhill of the Capo Berta when other riders went down in front of me and I couldn't avoid them. But I was fortunately able to get up and ride immediately. Then I crashed for the second time on the descent of the Poggio when someone crashed in front of Kwiato and I. At that point my race was over. It's a pity because despite the first crash, the idea was to ride to the end of the downhill of the Poggio and see what we could have done. I had good legs today and it's a shame I couldn't get to the finish and we couldn't play all our cards."
Stybar finished three minutes down, while Kwiatkowski crossed the line nearly two minutes later.
"Bad luck today, especially that both of us were on the ground," said Kwiatkowksi.
"The race looks different than what it could have been if that didn't happen. We did it perfectly today, my team-mates did a great job putting us into good position. For the first time at Milano-Sanremo I was there on the Poggio. We felt really comfortable. It was still a big group. When I heard Cavendish was no longer with us, I knew we both still felt good and who knows what can happen in this kind of race. Maybe we could try an attack or make the sprint ourselves. But again, bad luck, and not much I can do in this situation other than feel happy with my condition and that the crash was not worse."