Ellsbury lined a leadoff double to the wall, Jeter followed with a hard single and the Yankees beat Buehrle for the 12th straight time over a decade-plus, sending Toronto to its season-worst sixth straight loss, 5-3 Friday night.
The Yankees won their third in a row to preserve their faint playoff hopes. They began the day five games behind Oakland for the second AL wild-card spot, with Seattle and Cleveland also in the way.
"End strong, see what happens," Adam Warren said after earning a save.
Ellsbury homered, doubled and drove in three runs, but made an early exit. He hustled to beat a double-play relay as the Yankees took a 5-2 lead in the fourth inning, and left before the fifth with a strained right hamstring.
Manager Joe Girardi said he doubted Ellsbury would play Saturday against the Blue Jays and said it was a "distinct possibility" that he was done for the season.
The cheers for Jeter kept getting louder and louder during his final homestand, and fans chanted his name throughout the ninth inning.
Jeter delivered two singles, including one where he carried the shattered-off bat handle all the way to first base, and posted back-to-back multihit games for the first time since late July. The retiring captain later hit a long fly that really got the crowd hollering before it was caught on the warning track.
The 40-year-old shortstop also alertly tricked speedy Jose Reyes off second by bluffing a throw to first, trapping him in a rundown.
Buehrle (12-10) is winless in 17 starts against the Yankees since April 2004. His losing streak against New York is the longest by any pitcher against a single opponent since Bobby Witt dropped 12 in a row to Cleveland from 1991-99, STATS said.
Buehrle, who has 198 career victories, fell to 1-14 lifetime against the Yankees.
"That is the way it goes, it is almost getting to the point where you want to laugh it off," he said.
Reliever Esmil Rogers, who was waived twice this season by Toronto, retired Encarnacion on a bases-loaded grounder to end the seventh. Warren pitched 1 2/3 innings for his third save while closer David Robertson and setup man Dellin Betances got the night off.
Reyes doubled twice and singled. The shortstop threw wide on Ellsbury's RBI forceout, and the error allowed another run to score.
NICE JOB, KID
Canadian rookie Dalton Pompey got his first major league hit for Toronto in the second. Jeter got the ball back from the outfield and tossed it into the dugout, then gave the 21-year-old newcomer a slap on the back when the inning ended.
"He said, `Congrats, I hope for a great career for you," Pompey said. "And I said, `Thanks, it is a pleasure to meet you.' And he said, `Likewise, keep swinging it.' So it was good words from him."
"I just talked to Derek Jeter," Pompey said. "Surreal, right?"
Brett Gardner went hitless in four at-bats, striking out twice. Dropped to sixth in the Yankees' lineup, he's in a career-worst 0-for-27 slump.
Blue Jays: Encarnacion had an MRI on his back before the game. Manager John Gibbons said it flared up this week in Baltimore.
Yankees: DH Carlos Beltran played for the first time since announcing his wife had a miscarriage of the couple's son. Beltran left the team Monday and returned on Thursday. Girardi said "sometimes, for athletes, for anyone, it's good to get back out there, to doing what you're used to doing and living that normal life. But obviously he's got a heavy heart, and we've got a heavy heart with him." Beltran went 0 for 4.
Blue Jays: Rookie RHP Marcus Stroman (10-6, 3.80) starts on Saturday. He is currently appealing a six-game suspension imposed this week by Major League Baseball for throwing at the head of a Baltimore hitter in his last start. Gibbons said the team wants to get the matter resolved before the end of the season so there is no carry-over next year.
Yankees: LHP Chris Capuano (2-3, 4.55) is set to pitch against the Blue Jays for the sixth time this year. He faced them three times in relief with Boston, and has started twice against them for New York.