It was the largest number of runs that Kennedy has given up in a single frame this season.
"A three-run homer is a death blow a lot of times to a pitcher and to a game," Padres manager Bud Black said.
Kennedy was rolling early on. He set down the first nine batters he faced, and received a lead in the third after Will Venable launched his second homer of the season beyond the scoreboard in right field.
But things went south quickly for Kennedy.
The right-hander fell behind 3-0 on Ben Revere to lead off the fourth before Revere smacked double off the right-field wall. He advanced to third on a wild pitch, and Chase Utley drove him in on a single to left-center.
Then, after Ryan Howard singled, Byrd connected on his 10th home run of the season on Kennedy's 3-2 offering to cap a four-run inning and put the Phillies up 4-1.
"The middle of the order got him," Black said. "The pitch to Byrd was probably a little bit higher than he intended to throw it. He meant to throw a fastball down and away. He got it up just enough for Byrd to get extended and get the ball in the air to right-center. But besides that, I thought the overall stuff was good."
In 2011, Kennedy finished fourth in the National League Cy Young Award voting after going 21-4 with a 2.88 ERA for Arizona. He had endured two mediocre seasons before resurrecting himself this year. Kennedy saw his ERA rise to 3.63 after allowing five runs in seven innings.
"It's frustrating, but I talked to [pitching coach Darren] Balsley about it and seems like every time there's an outing like this, there's always one or maybe two pitches that you want back," Kennedy said. "The pitch maybe to Revere to lead off the inning. I fell behind on him and he got that double. You want to get that first guy of every inning. Utley did a good job of putting that ball in play. I thought the fastball would have bounced, but he put it in play and got a hit. And then fell behind again on Howard. Then the next guy, same thing."
After allowing 17 earned runs in his previous 20 innings, Phillies starter A.J. Burnett bounced back against the struggling San Diego offense. The right-hander logged 7 1/3 innings, allowing two earned runs on three hits and two walks while striking out three.
The Padres brought the potential winning run to the plate in the ninth inning, but closer Jonathan Papelbon escaped the bases-loaded jam to notch his 300th career save. Papelbon got Yonder Alonso swinging at strike three for the second out before pinch-hitter Tommy Medica grounded into a forceout to end the game.
"A lot of times, one pitch can make the difference in a game and in the ninth inning, Papelbon had to work his way through a stressful inning," Black said. "But we were one hit away from making that game really interesting. One ball in the gap or one ball in the seats from taking the lead. Loaded the bases against a guy whose been throwing the ball well. And they executed a pitch, and prior, we didn't. That's what the game came down to."