Ellsbury extended his hitting streak to 14 games the longest for a Yankees player since Jeter's 19-game streak in 2012 and gave New York just its fourth win in the last 11 games. Ellsbury's hit came after Jeter's ground-rule double that ended the night for Seattle starter Hisashi Iwakuma (4-3), who had not been threatened since the first inning.
Dellin Betances (4-0) got the victory in relief of New York starter Vidal Nuno despite giving up the lead in the bottom of the seventh on Dustin Ackley's RBI single.
David Robertson pitched the ninth for New York to pick up his 15th save.
The Mariners honored Jeter during a pregame ceremony in his final visit to the city where he made his major league debut in 1995. Jeter was given a seat from the old Kingdome and an engraved watch from former New York teammate Robinson Cano as part of his farewell tour gifts.
Jeter then went out and had two hits and scored two runs. He also scored on Carlos Beltran's RBI double in the first. Brian McCann added an RBI infield single. The Yankees have not scored more than four runs in the past 11 games.
Nuno and the Yankees bullpen made sure three runs were enough.
A rainout on Monday in Kansas City ruined a potential matchup between former teammates in Japan, Iwakuma and Masahiro Tanaka. Instead, Tanaka was pushed back to Wednesday.
Nuno went 5 2/3 innings and was in line for the victory before Betances' problems in the seventh. Nuno struck out two and allowed only Cole Gillespie's RBI single to score Cano in the first.
Nuno did escape trouble in the second and fourth innings when Seattle had runners in scoring position with two outs and were unable to get the runner home. Michael Saunders came inches from a three-run homer in the fourth, but his drive to the deepest point of Safeco Field was caught at the wall by Ellsbury.
Seattle did get Ackley's two-out line drive single over second baseman Brian Roberts to score Mike Zunino in the seventh.
Iwakuma was strong until the eighth. He threw 7 1/3 innings and allowed only five base runners after the first inning. He threw season-high 108 pitches, but made a mistake to Jeter with one out in the eighth and the double ended his night. Charlie Furbush entered and got ahead of Ellsbury before giving up the deciding hit.
Notes: Yankees RHP Shawn Kelley is expected to rejoin the club on Wednesday. Kelley's been out with a back strain. ... Seattle signed second-round pick OF Gareth Morgan on Tuesday. Morgan took part in batting practice with the team before the game. ... Seattle RHP Taijuan Walker (shoulder) was returned from his rehab assignment and optioned to Triple-A Tacoma.