With the theft, Ellsbury tied Tommy Harper's franchise mark of 54 stolen bases set in 1973. The 25-year-old fell just short of the record last season, stealing 50 bags.
After drawing a leadoff walk, the speedy center fielder took second base off Yankees starter Andy Pettitte, the same pitcher against whom Ellsbury stole home in thrilling fashion on April 26.
Nine of his steals this season have come against New York.
Ellsbury came around to score later in the first on a Victor Martinez sacrifice fly. He finished 1-for-4 with two RBIs and two runs scored in Boston's series-opening loss to New York.
John Barone is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.