Shields (10-7) surrendered one run, allowed one walk and struck out six in his encore to a three-hit shutout in his previous start against Oakland Wednesday.
Fernando Rodney finished up with a scoreless ninth for his 33rd save as the Rays took the opener of a three-game series.
Evan Longoria drove in a run with a sacrifice fly in his return from the disabled list with a hamstring injury, making his first appearance since April 30.
J.A. Happ (0-1) took the loss for the Blue Jays, yielding four runs on seven hits over 4 1/3 frames.
Colby Rasmus went 2-for-3 with a homer for Toronto.