Valverde made his return to the peloton during the 2012 Tour Down Under, the first race of the UCI World Tour season. He won the race's fifth stage – the queen stage of the event – by out-sprinting GreenEDGE's Simon Gerrans in a two-man sprint in Willunga, and finished second overall. He earned his first overall victory since his return, by winning February's Vuelta a Andalucia, as well as achieving a stage victory during the race. Valverde also finished third in Paris-Nice, and by winning stage 3 showed good form for the upcoming Tour de France. In the Tour de France he sat casually in the peloton until initiating a breakaway in stage 17, which he held onto after breaking away from the other 16 riders in the breakaway. Team Sky almost chased him down, ending only 19 seconds adrift. Hence Valverde won a 4th Tour de France stage of his career.
Valverde entered the Vuelta a España as a lieutenant to the defending champion Juan José Cobo in the Movistar team. However, Valverde would soon become the leader when it became apparent that Cobo was not in top form. His team Movistar started off with a victory in the first stage, a team time trial, of the Vuelta. Valverde would take the lead of the general classification, points classification, and combination classification after winning Stage 3, in which he chased down repeated attacks from Alberto Contador and outsprinted Joaquim Rodríguez at the finishing line. He would subsequently lose the lead to Rodriguez, but won the eighth stage atop the Collada de la Gallina in Andorra. Alberto Contador broke away from the small lead group and looked like he was heading for the win, but Rodriguez and Valverde passed him with less than 100 m (330 ft) to go, with Valverde taking the win. Valverde ultimately finished the Vuelta in second position overall after being a constant threat for the leader, which was Rodriguez until stage 17 where Contador soloed to victory and grabbed the lead, which he would not relinquish. Valverde also snatched both the Points Classification and the Combination classification jerseys from Rodriguez as a result of a sixth place finish on the very last stage in Madrid.
Valverde had to settle for a bronze medal in the World Championships in Valkenburg, as he was unable to reach Philippe Gilbert who attacked on the final climb of the Cauberg. He was the first of a group of 27 riders who had a five seconds deficit on the Belgian when crossing the line. He was supposed to participate in the Giro di Lombardia, but announced on the morning of the race that he was suffering from influenza and was putting an end to his 2012 season.
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