International Paralympic Committee (IPC) President Philip Craven said Russia's Paralympians were part of a broken system overseen by the Russian government and suspended the Russian Paralympic Committee ahead of the September 7-18 Games.
Russia immediately said it would appeal and condemned the move as violating the human rights of its athletes.
"Tragically this situation is not about athletes cheating a system, but about a state-run system that is cheating the athletes," Craven told reporters.
"I believe the Russian government has catastrophically failed its para-athletes. Their medals over morals mentality disgusts me."
The IPC decision follows revelations of widespread cheating in Russian sport which ignited a doping scandal that has threatened to split the Olympic movement and costs dozens of Russian sportspeople their place at the Rio Games.
The International Olympic Committee (IOC) stopped short of banning all Russian sportspeople from Rio and said on Sunday 278 of the original 387-strong Russian team would be able to compete after being cleared by their individual sports federations.
IOC President Thomas Bach had described a blanket ban as a "nuclear option" in which innocent athletes would be "collateral damage".
But the IPC had no such qualms and its hardline move drew praise from anti-doping authorities.
"The IPC showed strong leadership today in holding Russia's state-organised doping program accountable. Their unanimous decision goes a long way towards inspiring us all," said Travis Tygart, head of the U.S. Anti-Doping Agency.
