The 40-year-old bade a fond farewell to Yankee Stadium on Thursday, a walk-off single confirming a 6-5 victory for the Yankees over the Baltimore Orioles.
With the Yankees unable to make the post-season after a season of inconsistencies, suggestions had been raised that Jeter would skip the season-ending series.
However, Jeter has instead opted to end his shortstop career on home turf, and will go head-to-head with the Yankees' fierce rivals one last time after 19 years in New York.
Commenting after the Orioles game, Jeter announced: "I've played my last game at shortstop; today was my last game there.
"I want to take something special from Yankee Stadium, and the view from shortstop here tonight is what I want to take from it."
Jeter is to feature at Fenway Park this weekend as designated hitter and said the chance to bring the curtain down on his career in one of sport's most fiercely fought fixtures was too strong to turn down.
"Out of respect for the Red Sox, their fans and the rivalry, I'm going to play and DH," he explained.
"I'm not sure about tomorrow [Friday], but I will play, and hopefully people can respect my decision. I've only played shortstop my entire career, and the last time I want to play it is tonight."