Poland's Rafal Majka (Saxo-Tinkoff) took third place at the end of a 242-km trek from Bergamo to Lecco, with pre-race favourite Vincenzo Nibali of Italy crashing out.
Rodriguez attacked in the Villa Vergano climb with just under 10 kilometres left and never looked back, just like last year when he beat another Spaniard Samuel Sanchez.
Nibali, fourth in last weekend's world championships road race, was caught in a crash just ahead of the Muro di Sormano, a 1.9-km climb at an average gradient of 15.8 percent.
In the descent, Valverde and his Movistar team mate Nairo Quintana powered away from a group of favourites and were joined by three other riders.
Thomas Voeckler, looking to become the first Frenchman to win the Classic of the Fallen Leaves since Laurent Jalabert in 1997, joined them and attacked with 60 kilometres left.
He built a three-minute lead at the top of the Madonna del Ghisallo but was caught with 12 kilometres remaining, shortly before Rodriguez made his move.
The result meant Rodriguez overtook Britain's Tour de France champion Chris Froome, who pulled out with a back injury before the race, in the elite World Tour rankings.
It was the final race for American David Zabriskie, who heads into retirement after a 13-year professional career.
He was one of Lance Armstrong's former team mates who testified against the disgraced cyclist in the U.S. Anti-Doping Agency's investigation into the Texan.
Zabriskie, who also admitted to using performance enhancing drugs, was banned for six months as part of a plea bargain to provide sworn testimony to USADA.
(Reporting by Julien Pretot; Editing by Josh Reich and Alison Wildey)
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