Noguera has denied allegations he gave far-right paramilitaries a hit list of human rights workers and trade union activists, some of whom were later killed, while he was in charge of domestic security.
Judge Leonor Perdomo, a member of a council that reviews appeals, ordered Noguera's release after ruling he had been detained illegally on an arrest warrant from the attorney general's office.
Perdomo ruled the arrest illegal because Mario Iguaran, the chief prosecutor, had not personally issued the request that Noguera be jailed.
Iguaran said he was in "total disagreement" with the judge's decision and would continue his investigation.
"I don't think Colombia or the international community can tolerate the message that conspiring with criminals has any relation to one's functions as a public servant," he said.
The former intelligence chief is a key player in a scandal linking Uribe allies to paramilitaries founded in the 1980s by rich landowners looking for protection from Marxist rebels.
Human rights groups have accused the paramilitaries of working with politicians and army officers to murder and kidnap and to steal land in the name of fighting the Marxists.
Eight pro-Uribe politicians and a regional governor have been also jailed on charges they helped support former paramilitary groups who have now disarmed under a peace deal with the government.
Uribe, who has received billions of dollars in US aid to fight rebels and the illicit drug trade, says he welcomes the probe to cleanse his government.
The suspected ties to the paramilitaries date from before his presidency.
More than 31,000 fighters from Colombia's paramilitary movement have handed over their weapons under a 2003 peace deal with Uribe that grants short jail terms for full confessions and compensation for their victims.