The Galaxy took the lead in the third minute when Landon Donovan picked up a loose ball on the edge of the area and blasted the ball into the top corner.
Vancouver tried to get back in the game straight away and Gershon Koffie was unlucky to see his effort from distance go just wide of the post.
Johnny Leveron should have equalised for the Whitecaps but he drilled his volley wide of the target when well placed on the edge of the box.
After the break, Vancouver surged forward looking for a leveller and thought they had found one in the 81st minute when Kekuta Manneh struck a powerful shot that clattered off the bar. The rebound fell to Jordan Harvey but Penedo made an excellent reaction stop turning the ball wide.
The keeper's heroics were enough to earn the Galaxy all three points at BC Place.