The Spaniard threatened to take the red leader's jersey from Simon Yates (Mitchelton-Scott), coming within 25 seconds two days ago, but those thoughts escaped quickly in the last mountain test before the final Madrid finish. Valverde ended tough mountain day on the Coll de la Gallina down from second to fifth overall at 4-28 minutes.
"Today in the second ascent of Beixalis, I was suffering a lot," Valverde said. "I wasn't feeling at all good, and I could barely turn my legs. After that, all I could do was suffer and then suffer some more."
Valverde closed the stage 2-46 behind Yates, who should be crowned 2018 Vuelta a España king in Madrid on Sunday.
After an attack by team-mate Nairo Quintana (Movistar) and Miguel Angel Lopez (Astana), Yates responded at 17 kilometres out and put Valverde in the red zone.
Valverde had Movistar chase, Quintana dropped back, but he cracked in the effort to even catch Yates – much less put time into him. He started the day at 1-38 back, but ended much worse.
"You have to be happy when you give it everything you've got. You have to accept the defeats, when you win, everything is great, but when you lose, you have to recognise that your rivals are better and keep looking ahead," Valverde, the 2009 Vuelta winner said.
"But I've been up there through the whole Vuelta and I'm leaving happy, both for the team work, with our two stage wins, the points jersey and the teams prize."
Team Movistar faltered in their home tour after the Tour de France in July. They took three leaders with Valverde, Quintana and Mikel Landa but they ended only with a stage win by Quintana and seventh overall with Landa.
Quintana began the Vuelta as the standout favourite. Instead, Valverde took the team's leadership reins. It looked good before these last two days in Andorra.
"The team has been great throughout the whole Vuelta and Nairo has shown today he knows how to be a great team-mate and be by my side. I thank him for that," Valverde said. "It's painful to come off the podium, but when you give it everything, you can't ask for more.
"Now I have to look ahead to the Worlds, we have to see what we get there. These last few days have not been the best but I think there's time to turn things around and head to Innsbruck in good shape."
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