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Nadal tops Federer in Wimbledon thriller
San Francisco trailed 2-0 in the ninth before Bengie Molina's single and Steve Holm's pinch-hit double created the extra inning.
Vizquel and Molina both had two hits for the Giants, who had ended a six-game losing streak with a 6-5 victory Tuesday.
The winner was Tyler Walker (2-2). Brian Wilson earned his 14th save.
Colorado scored on Matt Holliday's first-inning RBI groundout and Jeff Baker's second-inning sacrifice fly.
Holliday was one of three players with two hits for the Rockies, who also lost twice in a three-game set against the Giants in April at San Francisco.
The losing pitcher was Matt Herges (2-1).