With the score tied 3-3, Todd Frazier led off the seventh with a single off Padres starter Clayton Richard (6-9) and Heisey followed by smacking a pitch over the left-center field wall for the decisive blow.
Drew Stubbs homered and finished with two RBI for the Reds, who remained one game behind first-place Pittsburgh in the National League Central following the Pirates' 3-1 win over San Francisco Saturday.
Homer Bailey (7-6) earned the victory after allowing four runs (two earned) on seven hits over 6 2/3 innings.
Richard surrendered six runs on eight hits over six full innings.
Chris Denorfia homered and Logan Forsythe went 3-for-4 with two RBI for San Diego.