Trentin's Mitchelton-Scott team said the 28-year-old Italian rider suffered a fracture in the thoracic region and will remain hospitalized for a few days.
"He passed away.in the presence of his family members and loved ones, who we keep in our thoughts".
Coming off his bike during a crash, France 3 reported that Goolaerts had to receive emergency CPR after suffering cardiac arrest.
David Lappartient, president of cycling's world governing body the UCI, said: "On behalf of the UCI and the cycling family as a whole, I would like to extend my deepest condolences to the family, team and loved ones of Michael Goolaerts, who left too early". "We share their huge sadness", Mr Lappartient wrote on Twitter.
Goolaerts rode in support of cyclo-cross world champion Wout van Aert of Belgium.
Paris-Roubaix victor Peter Sagan and second-placed rider Silvan Dillier were both fined 1000 Swiss Francs (CHF) for taking on "unauthorised refuelling" during the final 20 kilometres of the race.
Sagan thus became the first rider since Bernard Hinault in 1981 to win the Queen of the Classics in the rainbow jersey of a world champion.
The team later added: "No update on Michael Goolaerts yet. Such a sad news".
The 257-kilometer race, called the "Hell of the North", includes 29 sections of cobblestones, which require special control of the bicycle and more effort than a usual road 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 a year ago in a New Mexico race, and a French racer died months later.
The race was also marred by several crashes that ended the hopes of outsiders Sebastian Langeveld and Matteo Trentin close to the Trouee d'Arenberg sector.
French judicial officials launched an investigation Monday into the death of Belgian rider Michael Goolaerts during the Paris-Roubaix cycling race.