He was quickly placed back into custody to await extradition to California, where he faces child pornography charges, the Los Angeles Times said.
Boulder District Attorney Mary Lacy had pursued Karr's extradition from Thailand and from California, but dropped all charges against the former teacher.
Investigators tested DNA found on the little girl's underwear against Karr's DNA but found no match, The Rocky Mountain News said.
Karr was arrested in Thailand Aug. 16. Lacy said the action was taken to ensure an uncontaminated sample of Karr's DNA could be obtained.
"This case is not closed, and we will continue to investigate leads and pursue justice," Lacy said.
KUSA-TV, Denver, reported DNA tests "conclusively" excluded Karr.
Karr, 41, was extradited to Colorado after allegedly telling investigators he had accidentally killed JonBenet nearly a decade ago. The body of the 6-year-old girl was found in the basement of her family's posh Boulder home.
Investigators have focused much of their inquiry on the family but JonBenet's parents insisted an intruder was responsible. The girl's mother, Patsy, died earlier this year.