Mike McGee opened the scoring in the 16th minute after he collected the rebound of a Hector Jimenez header and fired it in from 3 yards out.
Then in the 30th, Donovan hit Robbie Keane with a pass inside the box and the Irish forward pounded it home from about 10 yards out to double the advantage.
Donovan capped the scoring 11 minutes later on a penalty kick as the Galaxy (6-8-2) moved back into the playoff hunt with their third victory in a week, climbing into fifth place in the Western Conference.
The third-place Whitecaps fell to 7-4-5.
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