The Phillies went 8-2 on their three-city, 10-day trip and improved to a major league-best 16-6 on the road.
Clay Condrey (4-0), the Phillies' sixth pitcher, worked two scoreless innings.
Chase Utley got the winning rally started with a two-out walk against Brett Tomko (0-1). Utley stole second before Ruiz lined the ninth pitch of the at-bat down the third-base line.
A strong contingent of Phillies fans in the crowd of 46,986, the biggest at Yankee Stadium since opening day, cheered wildly as Utley scored.
Melky Cabrera hit a tying single off Lidge in the ninth as the Yankees nearly rallied for their fifth walkoff win of a wildly successful 10-game homestand. New York went 8-2 in its best stretch to date at the new Yankee Stadium, and has won 10 of 12 overall.
Robinson Cano led off the ninth with a single to center off Lidge, who blew two save opportunities in the series. Pinch-runner Ramiro Pena then stole second before Cabrera hit a bouncer up the middle, just under the glove of diving shortstop Rollins.
Pena raced around to score the tying run without a play as Yankees fans prepared to celebrate another dramatic victory.
Cabrera stole second with one out and advanced to third on pinch-hitter Nick Swisher's grounder. But Lidge got Brett Gardner to bounce to first, sending the game to extra innings.
Lidge's ERA actually dropped to 9.15 after his fourth blown save in 12 chances this season. He gave up Alex Rodriguez's tying homer and Cabrera's winning single in the ninth inning of Philadelphia's 5-4 loss on Saturday.
New York put its first two batters on in the 10th but Condrey got Mark Teixeira to ground into a double play. After Rodriguez was intentionally walked, Pena flied out to end the inning.
Teixeira added to the new Yankee Stadium's growing reputation as a launching pad with a broken-bat, solo shot off Cole Hamels in the sixth. Hamels slowly shook his head in disbelief as the drive carried over the wall in left despite Teixeira's bat shattering, leaving him holding barely more than the handle.
It was Teixeira's 13th of the season and No. 87 at New York's $1.5 billion field, setting the record for most homers in the first 23 games at a ballpark. Houston's home, formerly known as Enron Field, set the previous mark in 2000, according to the Elias Sports Bureau.
Hamels allowed two runs and eight hits in six innings, outpitching CC Sabathia in a matchup of ace left-handers. Hamels is 2-0 with a 2.88 ERA in four starts this month.
Hamels' batterymate contributed on defense, too. Ruiz completely blocked the plate and tagged out Damon to end the third as he tried to score from second on a single.
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