The complaint alleged that Jeppesen "falsified flight plans to European air traffic control authorities to avoid public scrutiny of CIA flights".
The ACLU was representing five men who said that they were secretly flown to prisons outside the United where they were tortured.
General Michael Hayden, the CIA director, had called for the application of the US government's so-called "state secrets privilege", allowing intelligence agencies to prohibit courts cases using evidence that is said to jeopardise national security.
In public and confidential statements filed with the court, Hayden urged the judge to dismiss the lawsuit because he said that covert operations overseas could be exposed.
"The court's review of General Hayden's public and classified declarations confirm that continuing the case would jeopardise national security and foreign relations and that no protective procedure can salvage this case," Ware wrote in his ruling.
ACLU lawyers had argued that Hayden's security concerns were exagerrated because the existence of a rendition programme is publicly acknowledged.
Ben Wizner, an ACLU lawyer, said he would appeal against the decision.
"At some point, some court somewhere will have to determine the legality of the programme," he said.
George Bush, the US president, confirmed existence of offshore prisons in a speech in 2006, but declined to go into details.