He will be replaced on the cobbles by 24-year-old Slovenian Marko Kump.
Multiple Grand Tour stage winner Bennati pulled out of last Sunday’s Ronde van Vlaanderen with the problem.
"We have decided to take Marko into the team to Paris-Roubaix instead of Daniele," said sports director Lars Michaelsen.
"Daniele felt unwell... he has been heavily influenced by the extreme weather conditions in some of the spring races and never felt that he could hit his top level.
"It is a difficult decision for Daniele personally and for the team, but we also know that it is the right decision... we decided to give him a break from racing until he is completely fresh again."
The spring weather in Europe has been extremely cold after the opening races of the season in other, hotter parts of the world.
The team's line-up for Wednesday's Scheldepreijs remains identical to that of Paris-Roubaix, with the exception of Kump, who will not take part.
Saxo-Tinkoff line-up for Paris-Roubaix: Matti Breschel, Matteo Tosatto, Jonathan Cantwell, Michael Morkov, Anders Lund, Christopher Juul-Jensen, Jonas Aaen, Marko Kump