Donovan netted the only goal in the third minute of the clash at BC Place before Panamanian international Penedo came up with five saves, including a brilliant stop to deny Jordan Harvey in the 82nd minute after Kekuta Manneh had struck the upright.
The efforts of Penedo, who only joined the Galaxy from Municipal earlier this month, did not go unnoticed by Donovan who had some kind words for the 31-year old.
"In a game like this, you're expecting to need one big play from a defender or a goalie, or someone's going to need to make a play, because they were putting us under some pressure at the end," Donovan said.
"Fortunately, the first one hit the post. I was standing right behind it. I've played a lot of soccer games in my life, and when I see a play like that, I can't remember a time where a goal didn't occur after [that kind of rebound].
"It seemed like he just came out of nowhere, kind of like Superman, and extended his arm and made an unbelievable save."
The victory sent the Galaxy to second spot on the Western Conference table whilst Vancouver fell to sixth.