Ortiz (13-8) struck out five and walked three to outduel Masato Yoshii (7-8) and the surging Mets, who dropped one game behind NL East-leading Atlanta but still held a one-game lead over Houston in the NL wild-card race.
The Giants, coming off a 3-9 trip that ended in a sweep at Florida in which they blew four-run leads on three successive days, beat the Mets for the first time in four tries this season.
Aurilia broke a tie in the bottom of the fourth when he connected for his 17th homer, tying the San Francisco team record for most homers by a shortstop. Shortstop Daryl Spencer also had 17 homers in 1958, the Giants' first season in San Franisco.
Benard gave San Francisco a 3-1 edge in the fifth, driving a 2-1 pitch from Yoshii into the right-field seats for his 12th home run. Benard extended his hitting streak to a career-best 11 games and the longest by a Giant this year.
New York pulled to within a run in the seventh. Darryl Hamilton singled and Luis Lopez walked and they moved up on Rey Ordonez's sacrifice. Pinch-hitter Franco walked to load the bases and Henderson's RBI groundout scored Hamilton but Roger Cedeno grounded out to end the inning.
The Giants scored an unearned run on a rare error by New York, the majors' top defensive team.
Ramon Martinez hit a one-out double and J.T. Snow and Ellis Burks drew two-out walks. Bill Mueller hit a slow roller to second. Lopez, starting for Edgardo Alfonzo who was in Venezuela attending his uncle's funeral, charged the ball and tried to make a bare-handed pickup but dropped it for an error, allowing Martinez to score.
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