The 41-year-old American became the oldest ever winner of a grand tour in Madrid on Sunday.
The Spanish authorities had been asked to carry out the test on behalf of USADA and attended the hotel where the majority of Horner's RadioShack team were staying on Monday morning.
However, RadioShack confirmed that Horner was instead staying at a different hotel with his wife on Sunday night and had communicated his location, phone number and one-hour time window to be tested to the USADA.
"Chris Horner updated his whereabouts with USADA before the start of the final stage, giving the agency the name of his hotel for the night, phone number and room number for his one hour window between six and seven a.m.
"This is all according to the rules and Chris Horner received a confirmation email," they said in a statement accompanied with a copy of the said emails Horner sent to and received from USADA.
In response USADA admitted that there had been no wrongdoing on Horner's part and that they had not passed on the information regarding Horner's change of whereabouts before the testers visited RadioShack's hotel.
"In response to public statements from Team RadioShack today concerning Chris Horner, USADA can confirm that we were coordinating an out-of-competition test with the Agencia Española de Protección de la Salud en el Deporte (AEA) while Mr. Horner was in Spain.
"Mr. Horner properly updated his whereabouts information in advance of the test attempt, but given that the information was received in the United States, the AEA doping control officer on the ground in Spain did not receive the updated information prior to arriving at the hotel.
"This is not considered a missed test and neither anti-doping organisation provided information to the media regarding this situation."
Madrid's Olympic bid was questioned by the IOC partly because of the tarnished image of its anti-doping agencies.
After a four-month long court case earlier this year, blood bags seized from the disgraced doctor Eufemiano Fuentes were ordered to be destroyed rather than released in a doping scandal involving Spanish cycling teams.
"Spain is at the same level as all other countries fighting doping," bid leader Alejandro Blanco argued.
"We've had a problem in the past, but we have prosecuted the athletes as well as those who harmed the health of the athletes."