"I wish I could've erased (Davis) out of the lineup, that would've made it a lot better, but we won, that's the important thing," Kennedy said. "I threw everything at him, but it didn't make a difference. I can at least laugh at it now."
Davis, a Scottsdale Chaparral High School graduate and former Arizona State standout, became the seventh player this season to hit three homers in one game.
Meanwhile, Kennedy became the first pitcher in one of those games on the opposite side of the homers to earn a victory. The other six pitchers who started a game in which an opponent blasted three homers combined for a 10.87 ERA and an 0-5 record.
"It's bittersweet for sure," Davis said. "It's always good to feel good at the plate, but my ultimate goal is to win the game, and we didn't. I take it as a positive moving forward, but obviously you'd like to win."
Kennedy ended up tossing 6 1/3 innings, allowing three earned runs on seven hits while striking out nine to pick up his ninth win of the season.
Since the Cubs lit him up for six runs on July 13, Kennedy has won three straight starts.
"My command has been better," the 27-year-old said. "Being ahead of guys, it makes a big difference. I watched things on film and tried to think of drills we did in the past. It was getting frustrating, but it's working out now."
Gerardo Parra led the D-backs' offense with three hits, driving in two runs and scoring once.
"Parra gets discouraged when he doesn't play, but he always tells me he's ready," D-backs manager Kirk Gibson said. "He's got a great attitude. He's an aggressive guy and he's come a long way in all aspects of his game."
Just two batters into the bottom of the first inning, the D-backs took their first lead of the night when Aaron Hill gapped an RBI double to left-center field off Mets starter Chris Young, plating Parra, who led off with a shallow single.
After the Mets tied the game in the top half of the second on Davis' first homer, Ryan Wheeler answered back in the bottom of the frame with a double to center field, scoring Miguel Montero and giving the rookie his first Major League RBI.
Each starting pitcher put a zero on the scoreboard in the third, but in the fourth inning, Kennedy and Young both fell victim to the long ball.
Davis, who entered Saturday 0-for-4 in his career against the D-backs' ace, beat Kennedy for his second homer of the night off the center-field wall to pull the Mets to within one run.
But in the bottom of the inning, after Upton led off with a single, Montero smacked a towering two-run shot to right field, extending the D-backs' advantage to 5-2. Parra provided another insurance run with his third single of the game four batters later, driving in Wheeler.
In the sixth inning, Davis capped his night with his fourth long ball in two days, this time off a curveball from Kennedy.
"It's almost jaw dropping," Kennedy said. "I've never given up three to the same guy. He made SportsCenter, so there."
Takashi Saito, David Hernandez and J.J. Putz each pitched in scoreless appearances to close the night out and run the D-backs' bullpen scoreless streak to 13 2/3 innings.
The game, however, got tense at times for Hernandez and Putz, who both allowed the first two baserunners to reach base before retiring the side.
"I looked up and I had thrown 15 pitches without getting an out and I knew it would be a long night," Hernandez said. "Luckily, I just made pitches. I feel like as you mature, you learn how to react and adjust on the fly in situations."