After Todd Walker doubled, Boone hit an 0-2 pitch from Brandon Villafuerte (1-1) over the left-field fence nearly 6 1/2 hours after the first pitch, giving the Reds a sweep of the three-game series.
Jose Rijo (5-3), the Reds' sixth pitcher, tossed a scoreless inning for the win.
Cincinnati appeared to be cruising, opening a 7-2 lead on a sacrifice fly by Ken Griffey Jr. in the sixth.
But Bubba Trammell sparked the Padres' rally with a pair of homers. He hit a solo shot off Scott Williamson to make it 7-3 in the seventh, then tied the contest with a two-run blast off closer Danny Graves in the ninth.
It was Larkin's seventh homer of the year and his first since July 21, a span of 13 games.
Kearns' two-run single gave the Reds a 5-2 lead in the fifth and Cincinnati stretched its advantage in the sixth on Walker's RBI single and Griffey's sacrifice fly.
Notable deaths of 2014 [PHOTOS]
UPI Sports Results for September 19, 2014