Wheeler (3-1) turned in the best performance of his five-game major-league career, baffling the Giants on three hits while walking three and striking out five.
The rookie right-hander -- a former first-round draft pick of San Francisco -- tossed 64-of-101 pitches for strikes as the Mets pulled off their first sweep of the Giants since 1994.
Giants starter Matt Cain (5-6) didn't make it out of the first inning, getting roughed up for three runs while surrendering two hits and three walks.
Brandon Crawford went 2-for-4 with an RBI for reeling San Francisco, which has dropped four straight and eight of its last nine games.
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