Jones pulled a 2-1 pitch from Jamey Wright (1-2) far into the upper deck in left field with one out in the eighth, breaking a 1-1 tie and enabling Baltimore to avoid a three-game sweep at the hands of the Mariners.
The center fielder also saved a sure double with none out in the bottom of the fourth, making an over-the-shoulder grab against the wall of a drive by Miguel Olivo.
J.J. Hardy added a solo homer for the O's.
Jim Johnson (4-1) picked up the victory in relief of Brian Matusz, who limited the M's to one run on four hits in a 5 2/3-inning start, walking none and striking out three.
Seattle starter Michael Pineda pitched well but earned a no-decision, letting in only one run on six hits over seven frames.
Jack Wilson got the M's only RBI with a second-inning single.