The abuse included isolation, prolonged sleep deprivation, exposure to extremely cold temperatures and shackling in "stress positions" for prolonged periods of time, Padilla's lawyers said.
They also say he was threatened with execution and forced to consume mind-altering drugs "to act as a sort of truth serum" during repeated interrogations.
Cooke rejected the dismissal motion, saying it had no bearing on charges that he and two co-defendants provided material support for terrorism and conspired to murder, kidnap and maim people in Afghanistan, Chechnya, Bosnia and other countries.
The Pentagon and US justice department have repeatedly denied the alleged abuse of Padilla, an American convert to Islam.
"Mr Padilla fails to present a cognisable claim of outrageous government conduct entitling him to dismissal of the indictment"
Judge Marcia Cooke
Prosecutors accuse Padilla of training and associating with al-Qaeda before and after the September 11 attacks.
"Mr Padilla fails to present a cognisable claim of outrageous government conduct entitling him to dismissal of the indictment," Cooke said in her order.
She did not dispute the claim that Padilla had been abused and tortured, but said the argument for dismissal of the charges against him suffered from "numerous legal infirmities".
Padilla, 36, was arrested at Chicago's O'Hare Airport in May 2002 upon returning from Egypt.
He was accused by the Bush administration of planning to detonate a radioactive bomb, and classified as an "enemy combatant".
He was held without charge for three years and eight months before being indicted in a civilian court in November 2005 on charges that do not mention a bomb plot.