Bush presented Jeter, who is retiring after this season, with a farewell gift.
He posted a photo of the moment on his Instagram feed.
During a pre-game ceremony, video was shown of Bush at Yankee Stadium before Game 3 of the 2001 World Series, on Oct. 30, just weeks after the 9/11 terror attacks.
The former president presented Jeter with a framed signed photo of the two of them together in the batting cage at that World Series game.
Jeter, the long-time Yankees captain, is set to retire from Major League Baseball at the end of the season. The Yankees drafted him out of high school in 1992, and he first played in the major leagues in 1995.