The 23-year-old who was a rider for the Veranda's Willems-Crelan team fell on the second set of cobbles during the one-day classic in northern France.
"He passed away on Sunday evening at 22.40 in Lille Hospital in the presence of his family members and loved ones, who we keep in our thoughts".
It added that he "died of cardiac arrest, all medical assistance was to no avail".
David Lappartient, president of cycling's peak body UCI, offered his condolences to the rider's family. "We share their huge sadness", he posted on Twitter.
The Slovakian attacked 54 kilometers from the finish and bridged alone to the day's breakaway and drove the group to the finish.
Belgium's Michael Goolaerts was taken to hospital after crashing earlier in the race.
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2014 Paris-Roubaix victor Niki Terpstra (Quick-Step Floors) finished alone in third.
He rode several of the cobbled classics and semi-classics this season, finishing ninth at Dwars door West-Vlaanderen and 20th at both Kuurne-Brussels-Kuurne and Driedaagse De Panne. I'm exhausted after this race but not as exhausted as in previous years, when I didn't win it for some reasons, " Sagan said.
Team Sky: "Everyone at Team Sky is heartbroken by the loss of Michael Goolaerts. Such a sad news ...", Sagan wrote on Twitter.
According to the post-race Decision of the Commissaire's Jury sheet, both riders have been fined for breaking UCI race regulation article 12.1.040/23, which states that no unauthorised refreshment should be taken in the final 20km of a race.
There have been numerous deaths among professional cyclists while competing in recent years, including others by cardiac arrest. Two Belgians died in other races in 2016; American Chad Young died previous year in a New Mexico race, and a French racer died months later.