Hundley sent an 0-1 pitch from Micah Owings (3-4) into the left-field seats to give San Diego its second straight win after losing six in a row.
Hundley's shot, his second of the season, landed in the second deck to end the 5-hour, 14-minute game, the longest of the season in terms of time for both teams.
Rookie Luis Perdomo (1-0), the Padres' eighth pitcher, pitched three hitless innings for the first win of his major league career.
Owings, a starter pressed into action four days after working seven innings, threw 5 2-3 innings and allowed three hits. He struck out five and walked three.
The previous longest game by innings this season came earlier this month, when Seattle and Oakland went 15.
Last Memorial Day weekend, the Padres beat the Reds 12-9 in 18 innings in San Diego on Adrian Gonzalez's three-run homer.
The Padres scored twice in the eighth inning to tie the score at 5-all.
Gonzalez led off with a walk off against Arthur Rhodes. David Weathers replaced Rhodes and gave up a double to Scott Hairston before Jody Gerut grounded out to bring in Gonzalez. Weathers then walked two batters, sandwiched around an out, to load the bases.
Weathers walked pinch-hitter Drew Macias on a full count to bring in the tying run. Weathers thought he had Macias struck out earlier in the at-bat on a pitch close to the inside corner. The veteran reliever was visibly upset with home plate umpire Jim Joyce and the two exchanged words when Weathers was pulled.
Daniel Ray Herrerra relieved Weathers and retired Brian Giles to end the inning.
Laynce Nix and Jay Bruce each hit two-run homers for Cincinnati, which lost starting pitcher Edinson Volquez in the sixth inning with mild back spasms.
Nix connected in the fifth inning to give the Reds a 3-2 lead and Bruce hit his 11th homer one inning later, both off Josh Geer.
Volquez allowed two runs in the first inning, including Giles' leadoff homer, before he settled down.
The right-hander was cruising with two outs in the sixth inning before he walked Kevin Kouzmanoff. He ran the count to 3-0 on Hundley when he went behind the mound and appeared to be trying to stretch his back. He came out of the game before throwing another pitch with mild back spasms.
Volquez allowed two runs on four hits with three walks and two strikeouts.
Geer gave up five runs on five hits in 5 2-3 innings.
Notes:@ Giles' leadoff homer was the fourth of his career. The other three all came in 2007, the last on Sept. 30. ... Weathers was credited with a blown save making the Reds the last team in the majors to register a blown save for the second year in a row. ... Rhodes allowed an earned run, making Padres closer Heath Bell the only NL qualifying reliever who has not allowed an earned run. ... Padres RHP Greg Burke made his major league debut with one inning of scoreless relief.