De Marchi finished one minute 35 seconds ahead of Canadian Ryder Hesjedal (Garmin-Sharp). Frenchman Hubert Dupont was third in the same time.
"This is the best moment of my career," the Cannondale rider told reporters after winning with a time of four hours one minute 52 seconds.
"It is great to be in a break with such strong riders and this was a fantastic result."
Sky's Chris Froome, one of the favourites to win the race, fell before the first climb but suffered nothing more than a few cuts and was able to return to the peloton.
The Briton sprinted to the line and is fourth overall, 19 seconds behind Valverde (Movistar) who was ninth in Friday's stage.
Colombian Nairo Quintana is second overall, 15 seconds off the pace and three seconds ahead of Spain's Alberto Contador.
"We heard that Froome had fallen but we made sure that there were no attacks. In no way did we try to leave Froome behind as you have to have respect," Valverde told reporters.
"It was a difficult day. We had to be very careful because there were a lot of falls and it was dangerous but we finished well.
"It is tough in Andalusia. There was not so much heat today as yesterday, but still it was a suffocating."
Following the first of eight summit finishes on Thursday, the race favourites focussed on consolidation on a smoother course that provided an opportunity for the sprinters.
However, there were still ups and downs plus a 5-km climb to the finish in Alcaudete.
With 70-km to go there was a breakaway by Hesjedal, Dupont, Swiss Johann Tschopp and De Marchi.
Hesjedal looked strong but fell with 16-km remaining before staging a recovery.
(Editing by Tony Jimenez; editing by Toby Davis)
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