The veteran shortstop grounded a one-out hit into right field Sunday, chasing Blue Jays starter Drew Hutchison.
It was the 3,320th hit of Jeter's career, moving him past Hall of Famer Paul Molitor. Next on the list is Carl Yastrzemski, with 3,419.
One inning earlier, Jeter tied Molitor with a leadoff single, a line drive to right.
Jeter sat out Friday's series opener then went 0 for 2 with two walks Saturday. His previous hit was an RBI single in the fifth inning of Thursday's win at Houston.
Jeter entered play Sunday batting .182 with no homers and one RBI in what he has said will be his final season.
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