Valverde was the protagonist in the finale with an attack designed to contain new overall leader Miguel Angel Lopez (Astana) but which placed his team-mate Nairo Quintana in the hurt box.
The 38-year-old UCI Road World Champion went on to finish fifth behind the stage winner Angel Madrazo (Burgos-BH) while Quintana finished in eight place almost a minute behind López and at 23 seconds on GC.
"It wasn’t a failure by Nairo," Valverde said. "He remains strong and he lost time today, but it wasn’t so much. A failure would be losing five minutes if you ask me for an example.
"It was a climb that suited his characteristics well, but you’re not at the same level every single day.
"I tried to keep pushing, trying not to let ‘Superman’ go too far. Lopez was already the biggest favourite and confirmed it today.
"I had legs today, but it doesn’t mean anything, we continue to go day-by-day, and Nairo, of course, remains our GC contender for the race.”
Quintana, who was perhaps a surprise winner on Stage 2, said the decision for Valverde to go was made on the road as he took a defensive approach to the pace set ahead.
“Alejandro was strong and we had already talked between ourselves that we had to respect whoever was feeling the strongest of the two," Quintana said.
Happily, I didn’t lose too much time, and I hope to get my best legs back, I just didn’t feel great today. As soon as I get back to my previous form, I’ll for sure try to take advantage.
"I tried to defend myself today, I just lacked a bit of power."
Quintana attributed some of his sluggishness to a full season of racing plus the effort expended at the Tour de France where he won Stage 18 and finished eight.
"After the Tour de France, you don’t know how your body will react," he said. "I’ve been racing on full steam since the start of the season, and it’s normal that there’s some wear and tear at this point of the year.”
Stage 6 sees the riders take on the hilly 199km between Mora de Rubielos and tAres del Maestrat to an altitude of 1,195 metres above sea level.