Eric Hosmer delivered a go-ahead two-run single in the fifth.
The Blue Jays fell a half-game behind the first-place Orioles in the American League East, pending the outcome of the White Sox-O's game.
Duffy threw 101 pitches, 65 for strikes, and he gave up five hits and two runs, while walking two and striking out six over 6 2/3 strong innings. Peter Moylan turned in 1 1/3 shutout innings, and closer Kelvin Herrera registered his fourth save.
Blue Jays starter Aaron Sanchez gave up nine hits and four runs in his six innings.