In addition, the Russian Paralympic Committee was ordered to pay 10,000 Swiss francs (9,374 euros) in court fees.
"The appeal is dismissed," said a statement by Switzerland's highest legal body.
In addition, the Russian Paralympic Committee was ordered to pay 10,000 Swiss francs (9,374 euros) in court fees to the federal court and 12,000 Swiss francs (11,250 euros) to the International Paralympic Committee.
The IPC announced a month before the start of the September 7-18 Paralympics in Rio that the entire Russian team would be banned.
Russian officials immediately appealed to the Court of Arbitration for Sport (CAS) to have the decision overturned but that too was rejected.
On Wednesday, the Swiss court said that Russian allegations that CAS had failed to consider the cases of Paralympic athletes on an individual basis were unfounded.
Russia's track and field team were also banned from the Rio Olympics which took place earlier in the summer.