The throw from Ichiro Suzuki to the plate was too late to nail Ciriaco, and the Red Sox claimed the opener of a three-game series.
The rally made a winner of Andrew Bailey (1-0), who tossed a scoreless top of the ninth.
Dustin Pedroia went 3-for-4 with a solo homer and two RBI in the victory.
Derek Jeter smacked a two-run double for the Yankees, who fell into a first-place tie with Baltimore atop the American League East with the defeat.
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