Sagan finished second in the first Monument of the season, while Dowsett finished a credible 44th in the second group on the road, in just his second edition of the calendar's longest race.
The race's final climb, the Poggio, was where Sagan made his move and was joined by eventual race winner Michal Kwiatkowski (Team Sky) and Julian Alaphilippe (Quick-Step Floors).
Dowsett kept pace on the Poggio with the leading group, but described the moment when Sagan attacked.
He said: "For the Poggio, you have to stay in the wheels and stay on top of your power. I didn’t look at the power meter once, but I’d probably be surging at 600 watts or 700 watts and then backing off to 300 watts or 400 watts.
"I’m not a climber, and I knew that at 600 watts, I wasn’t going to last long, but it’s Milan-San Remo and you have to hang in.
"You grab a rest and get ready for the next surge - or for Sagan to accelerate."
He raced the two cobbled Classics in 2013 and 2014, but failed to finish on all four occasions.
However, the Essex time trialist is confident that he can make it to Roubaix's velodrome on April 9.
“They are special races, don’t get me wrong,” he said. “The buzz around Flanders is unbelievable.
"I’ve raced Paris-Roubaix twice and reached the Arenberg Forest and then pulled the pin.
“I’m in better condition now. Roubaix is one to tell your grandkids that you finished. I want to give it a good crack and just get to the showers. It’s important for me; it’s a rite of passage."
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