Marco Estrada tossed three-hit ball into the seventh inning against the suddenly slumping Yankees, outpitching Masahiro Tanaka during Toronto's second consecutive shutout.
In a series that featured the top two offences in the majors, New York mustered only one run and went scoreless over the final 26 innings. Not since 1999 had the Yankees been blanked in two straight games.
With their 11th win in 12 games, the streaking Blue Jays pulled within 1 1/2 games of the first-place Yankees. It was the first time since May 2003 that Toronto swept New York in a series of at least three games.
On an agitating afternoon for the Yankees, Brett Gardner slammed down his helmet with two hands after grounding out with a runner on second to end the third.
The next inning, he was hit in the back by Bautista's home run ball when a fan in the left-field stands threw it back onto the field.
Estrada (10-6) kept New York's dangerous lineup off balance all day, masterfully mixing his 77 mph changeup with a 90 mph fastball and slow curve. He gave up three singles and three walks, striking out six.
The right-hander was lifted after 89 pitches with two on in the seventh. LaTroy Hawkins got out of the inning, Aaron Sanchez pitched a hitless eighth and Roberto Osuna worked a perfect ninth for his 10th save.
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Donaldson homered into the Yankees' bullpen in right-centre on the seventh pitch from Tanaka (8-5), who yielded three hits in six innings. The right-hander was relieved after 80 pitches.
Bautista connected in the fourth, launching a mammoth drive that struck the facing of the second deck in left field.
Donaldson also went deep in the first inning Friday night, when Bautista's homer in the 10th sent Toronto to a 2-1 victory in the series opener.
Blue Jays: 1B-DH Edwin Encarnacion, who is 5 for 10 with a home run against Tanaka, sat out because of a tender finger on his left hand. Encarnacion's middle finger has been bothering him for a while, and he aggravated it on a swing Saturday. The team hopes Encarnacion will feel better after the off day Monday, manager John Gibbons said. The slugger has reached base safely in 16 consecutive games. ... DH Chris Colabello writhed on the ground for a frightening moment after getting hit by a high fastball from Adam Warren in the seventh. But replays showed the pitch mostly caught Colabello's elbow guard, and he remained in the game.
Yankees: With the Yankees scheduled to play 16 days in a row beginning Tuesday, manager Joe Girardi confirmed the club probably will plug in a spot starter at some point to give the rotation extra rest. He said right now he expects it to be someone currently on the staff, making RHP Bryan Mitchell and perhaps Warren the most likely candidates.
Toronto optioned reserve infielder Munenori Kawasaki to Triple-A Buffalo to open a roster spot for utility infielder Cliff Pennington, acquired Saturday in a trade with Arizona. Pennington made his Blue Jays debut and struck out as a pinch hitter with the bases loaded for the second out in the seventh. He stayed in to play second base.
Blue Jays: RHP Drew Hutchison (10-2, 5.42 ERA) starts Tuesday night at home against Oakland rookie Kendall Graveman (6-7, 3.90), one of four players Toronto traded to the Athletics for Donaldson last November.
Yankees: Top prospect Luis Severino makes his second major league start Tuesday night in Cleveland against RHP Carlos Carrasco (11-8). The 21-year-old Severino threw five impressive innings Wednesday in a 2-1 loss to Boston.
Mike Fitzpatrick, The Associated Press