Bonner, who had 11 rebounds, scored 13 points in the second half to help Phoenix (5-19) defeat the Storm for the first time in four games this season.
Camille Little had 11 points to lead Seattle (11-14) while Tanisha Wright added 10 points and eight rebounds. Reserve Tina Thompson had 10 points.
Lauren Jackson shot just 2 of 8 from the field and had six points for the Storm while Sue Bird was 3 of 9 from the field and finished with eight points and eight assists.
The Mercury broke from a 54-all tie by outscoring Seattle 13-2 to start the fourth quarter.