Valverde picked up a total of 12 bonus seconds on the day thanks to the stage win and an earlier intermediate sprint, but Porte didn't lose any more time on the hilly 126.6 kilometre circuit around Barcelona to win by four seconds.
Victory continued Porte's fantastic early season form having also won his second Paris-Nice title just two weeks ago.
France's Bryan Coquard was second in the stage just ahead of Russian Sergei Chernetski, who won his first World Tour stage on Saturday.
Italian Domenico Pozzovivo was just a second behind Valverde in third overall with two-time Tour de France winner Alberto Contador a further two seconds adrift in fourth.