Suzuki and Overbay scored when Ellis dropped a fly ball by Jayson Nix in shallow right field. Yasiel Puig came running in as Ellis was tracking the ball with his back to the rookie, whose left hand struck Ellis' glove as the ball dropped.
"It was just a pop-up in a weird spot and I dropped it," Ellis said. "I heard him at the last minute, but it was too late to get out of the way. It's a play that we have all the time. It's hard to hear out there."
Mariano Rivera retired the side in order while striking out two in the ninth to earn his 34th save in 36 chances in his farewell season.
Dodgers manager Don Mattingly was ejected in the ninth for arguing a checked swing call on Overbay.
Former Dodgers pitcher Hiroki Kuroda and current Los Angeles ace Clayton Kershaw dueled for much of the game, with neither allowing a run. Both gave up five hits -- all singles.
Kuroda struck out eight and walked one in seven innings in returning to Dodger Stadium for the first time since 2011.
"It was a little bit strange, but once the game started I was able to get into a rhythm," Kuroda said through a Japanese translator. "The Dodgers have a great lineup and I needed to be on my A-game."
Kershaw struck out five and walked none in eight innings to lower his major league-leading ERA to 1.87.
Jeter went 0-for-7 with a walk as the Yankees gained a split in the two-game series.
"We've been battling since I've been here," he said. "Hopefully, we can build on this."
Both teams had scoring chances in the seventh and eighth innings.
The Yankees had runners on first and second with two outs in the eighth when Brett Gardner flied out to left field for the third out.
The Dodgers had runners on first and second with two outs in the seventh before Skip Schumaker struck out swinging to end the inning.
Yankees 3B Alex Rodriguez was scheduled to play a minor league rehab game in Tampa, Fla., on Thursday, but Yankees manager Joe Girardi had no timetable for his return to the team. ... Yankees OF Curtis Granderson was expected to travel to San Diego on Thursday and be activated for Friday night's series opener against the Padres. ... The Dodgers gifted Rivera with a custom fishing pole and a $10,000 donation to his planned church in New York. Rivera met with a select group of Dodgers employees to talk baseball as part of his farewell tour. ... The Dodgers acquired C Drew Butera from Minnesota for either a player to be named or cash considerations. Butera was optioned to Triple-A Albuquerque. ... Celebrities at the game included Kobe Bryant and LL Cool J in Magic Johnson's box, Christina Aguilera, Samuel L. Jackson, Billy Crystal, Penny Marshall, Cristiano Ronaldo of Real Madrid, and Dallas Cowboys teammates Jason Witten and DeMarcus Ware. ... The two games against the Yankees drew combined sellout crowds of 105,460, making it the highest-attended two-game set at Dodger Stadium since 107,851 saw two games against Seattle on Aug. 30-31, 1997.
From Elias: Yasiel Puig has 71 hits and 10 homers in 49 major league games (entering Wednesday).
The last player with at least 70 hits and 10 homers in his first 50 games in the majors was Joe DiMaggio in 1936 (87 hits, 10 homers).