The Yankees fell 4 1/2 games behind AL East-leading Toronto. They didn't lose ground in the wild card race pending Texas' game against Oakland.
Nova threw two wild pitches, hit two batters, and gave up three extra-base hits in the second. The inning also included a passed ball by John Ryan Murphy.
Ryan Goins' RBI single started the rally, followed by Cliff Pennington's two-run homer. Russell Martin had a two-run double after Jose Bautista doubled home a run.
The Blue Jays tacked on four in the seventh thanks to a five singles and a walk, including a two-run infield single by Ben Revere.
Brett Gardner hit two three-run homers, one in the fifth and the other in the eighth.
The game was delayed in the sixth for 33 minutes.
The Yankees will try to avoid a four-game series sweep Sunday as Masahiro Tanaka (11-6, 3.57) faces R.A. Dickey (10-10, 4.01) at Yankee Stadium (1:05 p.m.).