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NEW YORK -- A-Rod vs. K-Rod, fans on their feet. Big Apple bragging rights on the line.

The grand finale of this Subway Series was good enough for Broadway.

With runners at the corners in the ninth inning, Francisco Rodriguez struck out Alex Rodriguez on a full-count changeup to preserve a 6-4 victory for Johan Santana and the New York Mets against the New York Yankees on Sunday night.

"I really enjoy that situation," Francisco Rodriguez said. "That's what I get paid for. Not to make the fans suffer like that, but to get the job done."

Jason Bay homered twice off an ineffective CC Sabathia, and the Mets held off the slumping Yankees in a tense finish to take two of three games at home in Citi Field.

"Right where you want to be. A great matchup, a great battle," Alex Rodriguez said. "It was a good sign we put some pressure on them. After being down 6-0 it came down to the last at-bat. I'll take my chances."

Shut down nearly all night by Santana, the Yankees rallied for three runs in the ninth to set up the juicy matchup of record-setting closer against MVP slugger.

After falling behind 2-0 and 3-1, K-Rod came back to even the count. A-Rod fouled off two more offerings before swinging through the eighth pitch of the at-bat.

"It was a pretty good one," said Santana, who watched on television in the clubhouse. "Pretty intense, but a pretty good one."

Alex Cora, a late addition to the lineup, hit a two-run single in a four-run second and the Mets took their first Subway Series since a rain-shortened two-game sweep at old Yankee Stadium in May 2008.

The city rivals meet again in the Bronx from June 18-20.

With a two-run shot in the second and a leadoff drive in the fifth, Bay tripled his home run total in his first season with the Mets. The All-Star slugger signed a $66 million, four-year contract in the offseason after hitting 36 homers and driving in 119 runs with Boston last year.

"Kind of like a big exhale," Bay said. "Hopefully, it's not a novelty anymore."

Bay broke out against the banged-up Yankees, who have dropped five of six to fall six games back of first-place Tampa Bay in the AL East. He went 4 for 4 and scored three times in Saturday night's 5-3 victory, then followed it up with another perfect night at the plate in front of a Citi Field-record crowd of 41,422.

"The ball was coming out of my hand pretty good and I had good action on my pitches, but I made some wrong decisions," Sabathia said.

Bay was hit in the back by an off-speed pitch from Sergio Mitre in the sixth. Plate umpire Marvin Hudson warned both teams, drawing arguments from Mitre and Yankees manager Joe Girardi.

Mets reliever Ryota Igarashi, just off the disabled list, dusted Kevin Russo with a high fastball in the ninth.

Santana (4-2) was sharp from the start in a marquee matchup with Sabathia (4-3), earning his first win in five outings since April 27 against the Los Angeles Dodgers.

The two-time Cy Young Award winner yielded six singles in 7 2/3 innings. He struck out five and did not go to a three-ball count until walking Nick Swisher with two outs in the seventh.

Francisco Cervelli followed with an RBI single off the top of the wall in the left-field corner, spoiling Santana's shutout bid. Cervelli thought the ball was a home run and umpires went inside for a look at the replay, but upheld the initial call.

"I think Citi Field is a little big for me," Cervelli said.

Santana was pulled after a pair of walks in the eighth. Pedro Feliciano retired Robinson Cano on a bases-loaded popout to preserve a 6-1 cushion.

Igarashi gave up an RBI single to pinch-hitter Juan Miranda before Francisco Rodriguez got two outs for his eighth save in 10 chances.

Derek Jeter greeted K-Rod with a run-scoring double, and Brett Gardner hit a slow RBI grounder to third. David Wright threw out the speedy Gardner on a close play, prompting arguments from Gardner and Girardi, who kicked at the dirt near first base.

Mark Teixeira reached on an infield single, setting the stage for Rodriguez vs. Rodriguez.

K-Rod also earned a five-out save Saturday night, combining for 49 pitches in the two outings.

Game notes

Cora filled in at 2B for Luis Castillo, scratched because of his sore left foot. ... Yankees RHP Javier Vazquez is slated to start Thursday night at Minnesota despite a bruised right index finger. Vazquez's bullpen session, however, was pushed back a day to Tuesday to give his finger more time to heal. He bruised the finger while bunting Friday night.