The Swiss claimed his fourth career trophy, three of which have come on clay.
The 28-year-old last won a tournament at Chennai in January two years ago.
Ferrer, ranked fourth in the world, was burdened by 31 unforced errors in the 64-minute loss.
The win was the second for Switzerland at the tournament after Roger Federer lifted the 2008 title and played the final two years later.
"I'll have to tell Roger to come back and play here again, everyone seems to want him to return," joked Wawrinka.
"As for me, I'm happy to be back here, I've had a good week on the clay."
The world number 16 was playing in Portugal for a second straight year after losing in the 2012 semi-finals to Juan Martin Del Potro, the defending champion whom Ferrer replaced in the draw after the South American fell ill with a virus.
"It was the perfect match for me," said Wawrinka, whose picturebook backhand served him well on a sunny afternoon.
"It's so tough to play David, he's a big champion."
Wawrinka used his most lethal stroke to best advantage in an opening set in which he kept Ferrer under the cosh throughout.
The top-seeded Spaniard did not even get onto the scoreboard until the 25th minute of the 29-minute opener but made it more of a contest in the second set.
His rally, however, came to an end as Wawrinka secured a break for 5-4 and served out the victory a game later. The Swiss won with three breaks of Ferrer while never facing a break point on his own serve.
"Stan played a great match, he deserved to win," said Ferrer.
"There have been a lot of Spanish champions here and I wish I could have been one of them.
"But I still had a good week, especially after coming in on the wild card. It was all positive. I had hoped to win but I still made the final and got matches on the clay."
Ferrer stood 5-1 on clay against Wawrinka and had beaten the Swiss in February for the Buenos Aires title.
Ferrer's loss still keeps him atop the ATP with 28 match wins this season. Wawrinka earned his 20th victory of 2013 as he played his 11th career final.