Santana followed R.A. Dickey's second one-hitter in a row with his best outing since he tossed a no-hitter on June 1. Jordany Valdespin added a two-run single for New York, which won by the same score Monday night in the series opener - a rematch of the 1969 World Series won by the Miracle Mets.
It was the second time this month that Santana and Dickey have thrown back-to-back shutouts. Dickey followed Santana's no-hitter against St. Louis by blanking the Cardinals. The two then flip-flopped in the rotation to give Santana extra rest after he threw a career-high 134 pitchers in the franchise's first no-hitter.
Santana (5-3) had a pair of shaky outings after that, but he was back in fine form against the suddenly punchless Orioles.
Making his first start at home since the no-hit gem, the left-hander allowed four hits and struck out five. He pitched around a leadoff double in the second inning and struck out consecutive batters with runners on second and third to wriggle out of the fourth.
Fans in attendance received a T-shirt featuring a picture of Santana with his arm raised moments after his no-hitter.
Bobby Parnell, Miguel Batista and Jon Rauch each worked an inning to finish the five-hitter and extend Baltimore's scoreless streak to 21 innings, dating to Sunday's 2-0 victory in Atlanta.
The Orioles, who had won seven of eight before arriving at Citi Field, were shut out in consecutive games for the first time since April 2005. They haven't homered in five games, their longest stretch of the season.
New York manager Terry Collins stacked his lineup with eight left-handed hitters against Tommy Hunter (3-4) and it paid off.
Daniel Murphy drove in the first run with a groundout when first baseman Mark Reynolds made a diving stop of his bases-loaded smash in the fourth. Valdespin singled to start the sixth, and Duda hit a high fly that nestled onto the netting that protects fans sitting just behind the 375-foot sign in right.
It was the second big homer in two nights for the Mets that wouldn't have cleared the Citi Field fences before they were moved in this season.
Valdespin added a two-run single off left-hander Dana Eveland with two outs in the seventh. The rookie started in left field after playing second base in Monday night's game, when he had a triple and double.
"He's adding some spark. He's adding some energy," Collins said before the game. "The last few games he's played, we've won."
NOTES: Baltimore OF Nolan Reimold, on the 60-day disabled list with a herniated disk, saw another specialist. Reimold and the Orioles are discussing his options with doctors. Season-ending surgery is a possibility. "We're trying to exhaust all possibilities with different people who have dealt with this to make sure we get a real good evaluation," manager Buck Showalter said. ... Baltimore blanked the Braves twice in a row before coming to New York. ... Collins said he would like to rest SS Omar Quintanilla on Wednesday night, though Collins is a little concerned about playing Justin Turner at shortstop because he just returned from a sprained ankle. Quintanilla singled leading off the seventh to snap an 0-for-16 slide. ... The Mets honored the Stony Brook baseball team, which became the first squad from New York to reach the College World Series since St. John's in 1980. ... Security apprehended a fan who ran on the field in the eighth without further incident.
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