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The world number one had won 11 of 12 previous meetings against the veteran Czech, and he improved that record with a 6-2 6-4 victory in Toronto.
Djokovic put Stepanek under pressure from the outset, turning it into a comfortable win after one hour, 28 minutes.
With his win, the three-time champion set up a quarter-final meeting with Tomas Berdych.
Djokovic broke twice in the opening set, taking a 4-1 lead before closing it out on the back of 20 unforced errors from Stepanek.
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The players traded breaks in the second before Djokovic saw out victory in the 10th game, an outrageous lob on match point sealing his win.