Darren Mattocks produced a Vancouver goal in the 3rd minute and the Whitecaps made it stand up for more than an hour in their bid to pull off the upset.
Los Angeles, however, turned a corner kick in the 69th minute into a goal by Magee, who lifted a shot into the top, left corner of the net from the center of the penalty area.
Donovan then converted a penalty kick which was awarded when he was taken down from behind in the box by Martin Bonjour.
The Galaxy will next take on San Jose in the Western Conference semifinals. Los Angeles will host the opening game of the two-game, aggregate-score series on Sunday.
The other conference semifinal series will begin Friday when Real Salt Lake visits Seattle.
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