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 30-year-old Porte's fantastic early season form having also won his second Paris-Nice title just two weeks ago.
"It's unbelievable to be honest," said Porte, who was also second on home soil at the Tour Down Under to start the campaign.
"It's capped off a pretty awesome start to the season - starting from Down Under to now. I really couldn't have imagined it would go this well after the year I had last year."
Porte stands at the top of the World Tour standings and is confident of a strong showing at his first major target of the season at the Giro d'Italia in May.
Indeed with the exception of Valverde the other four riders to finish in the top six - including two-time Tour de France winner Alberto Contador - will also line-up in the Giro, the Tour of Catalonia is a race considered ideal preparation for the challenge of the Italian race.
"We've got a good little run-up to the Giro so we can hopefully hit that in top form. I'm quite confident now that I can go there and fight for the podium," said Porte.
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.
"We wanted to try and get the overall win and we fought all day for it, although we knew it was going to be very, very difficult," said Valverde.
"We go away from here with three victories and second in the general classification, so you can't ask for more. It was a very balanced race."
An early three-man breakaway group of Marek Rutkiewicz, David Arroyo and Walter Pedraza was kept in check by Movistar as they looked to set up Valverde for a push at winning the general classification.
The 34-year-old then made his move on the last of eight laps up the Alt de Montjuic with five kilometres to go, but quickly abandoned any hopes of making a solo run to the line as Pozzovivo and Porte followed him.
Irishman Dan Martin attacked two kilometres later, but he too was caught in the final few metres as Valverde had just enough power to get to the line first in a congested sprint finish.