Trailing 2-0 in the sixth, the O's erupted for four runs to take control.
One out later, Jones sent an 0-1 pitch over the right-field wall for a three-run shot.
The blast made a winner of Chris Tillman (3-4), who held the Blue Jays to two runs on four hits and a walk over seven innings. He struck out five.
Toronto's Brandon Morrow (8-6) was tagged with the loss, yielding six runs (three earned) on four hits over 7 2/3 innings.
Colby Rasmus socked a solo homer for the Blue Jays.
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