In the process, the Reds snapped the Padres' season-best six-game winning streak.
While the Reds' bats produced the big hits, it should be noted that starting pitcher Bronson Arroyo (4-5) did more than simply carry his weight.
Arroyo allowed zero runs in a complete-game victory. He allowed three hits, walked one and struck out eight. Arroyo allowed a single in the second inning to Yasmani Grandal, a single to Will Venable in the fifth inning and a single to Chase Headley in the ninth inning.
But that's it.
"You only get one of those games like that every couple of years where everything is just going your way." Arroyo said. "For me, pitching with my head has always been my game. Those guys were a little messed up tonight. I beat guys with pitches I usually don't beat guys with -- 87 mph on the outer half and guys being late and stuff.
"That was basically just mixing up the pitches good enough for them not to be knowing what's coming. That's the biggest complement for me to go out there and have a game go like that."
And so it was for the Padres' offense, which hadn't managed three or fewer hits in a game since May 27 before Friday.
"It's an assortment of off-speed pitches we couldn't get the timing on. He throws the ball from a couple of different arm angles. He's just extremely deceptive," Padres manager Bud Black said. "That's his style."
Arroyo is now 3-2 with a 2.13 ERA in six career starts -- spanning 42 1/3 innings -- at Petco Park. This was the 13th complete game of his career.
"All his breaking stuff and his changeup are different speeds, so it's just tough to make the adjustments. That's just what he does. He had a great feel for everything tonight and made all the pitches he needed to make," Venable said.
The guy across the way from Arroyo, Padres starting pitcher Kip Wells, wasn't bad either, though his line took a hit in the seventh inning after he walked Frazier and then allowed a two-run home run to Hanigan that ended his night.
Wells, the 35-year-old who is pitching in the big leagues for the first time since 2009, allowed three runs on seven hits with three walks and three strikeouts over six-plus innings.
"Wells did a nice job," Black said. "He did better as the game went on, 1-0 through six innings ... we'll take our chances there."
Wells (1-2), coming off a start in Colorado where he tossed seven scoreless innings, allowed a home run to Cozart to start the game before settling down. Wells scattered five hits over the next five innings and trailed 1-0 entering the seventh inning.
A leadoff walk to Frazier opened the door for Hanigan, who hit a ball that barely made it over the fence in left field.
"For the most part, they barreled a couple balls, but by and large they hit [two] home runs off me and [they] were within 5 feet of still being in the field of play, so that's kind of unfortunate, but it happens," Wells said.
The Padres, who entered the game tied with the 1984 Dodgers and the 2012 Marlins as the only teams with pinch-hit home runs in three consecutive games, came up empty on Friday. Logan Forsythe was the only pinch-hitter used and he grounded out in the eighth inning.
That the shutout came at the hands of the Reds was not surprising, as Cincinnati pitchers already have three shutouts on this 11-game road trip and five for the season.