The Sicilian, who won the Vuelta in 2010 and in May added the Giro d’Italia to his palmares, was judged to have finished with the same time as the two-man breakaway that contested the finish.
Daniel Moreno (Katusha), the winner in April of La Flèche Walloone, was first across the line at the summit in Fisterra at the climax of a gruelling 189km stage.
The Spaniard, a pure climber riding ostensibly riding as super domestique to last year’s world number one, Joaquim Rodriguez, was chased across the line by Fabian Cancellara, a four-time world time trial champion, and cobbled Classics specialist.
“When 55kg are jumping away it’s different from 85kg going,” the Swiss powerhouse joked afterwards.
The drama continued to unfold after the first and second-placed riders had crossed the line.
A group containing most of the pre-race favourites, including Nibali, was awarded the same time as Moreno and Cancellara, despite the visible gap.
Horner, who yesterday became the oldest rider in the history of the sport to win a stage of a Grand Tour, finished after the favourites’ group, in a time officials judged to be six seconds slower.
Horner said he was unconcerned by the loss of the leader’s jersey, adding that he planned to regain it when the race returned to the mountains.
“I’m going to always remember yesterday and how it felt to take the jersey but the important day to have it is at the end,” he said.
“It’s not ideal for the sponsors to lose the jersey of course, but it’s ok for now and I will use my good legs to get it back. I plan to have a fantastic Vuelta.”