"You have certain people on teams you try to make sure they don't beat you and he's the guy on this club," Hale said.
Upton's home run in the fifth inning came with two outs and first base open in a 2-all game. Hale said in that situation, it was his fault for not calling for an intentional walk to Upton.
"I just kick myself in that situation," he said. "Either walk him on four pitches or make it clear to our guys that he's not supposed to beat us."
Hellickson also blamed himself.
"I just have to make a better pitch to that guy in that situation," Hellickson said. "If I walk him, it's fine. It wasn't a terrible pitch, but it wasn't good enough pitch right there."
Upton connected for his 14th home run on a full-count pitch from Hellickson, who allowed seven runs and 10 hits in 5 1/3 innings.
Cashner (3-9) hung tough as he held the Diamondbacks to two runs and eight hits. The right-hander escaped a bases-loaded, one-out jam in the second unscathed and got out of the third inning after allowing three consecutive doubles.
Cashner, who struck out six and did not walk a batter, struck out Chris Owings and got Hendrickson to ground out in the second to hold Arizona from scoring.
Cashner won for the first time since May 27, a span of six starts, and also drove in a run with a bunt single.
San Diego last won consecutive games during a four-game streak June 2-6. The victory moved San Diego ahead of Arizona into third place in the NL West. The Padres are 5-6 since Murphy took over after Bud Black was fired.
Upton's homer was his 11th at Petco Park and his first since he homered on June 13 to give the Padres a 2-1 win over the Dodgers.
Will Venable and Clint Barmes led off the sixth with singles, and with one out, Cashner laid down a bunt between the mound and the third base line. Hellickson fielded the ball, but Venable slid home ahead of the tag.
In four starts this season against San Diego, Hellickson is 1-2 with a 7.55 ERA having allowed 31 hits in 22 2/3 innings.
Hellickson came in having allowed no unearned runs while Casher had given up a major league high 19 unearned runs, 11 more than the next closest pitcher.
NEARLY PERFECT VS. PADRES
Goldschmidt has reached base in 26 of his last 27 games against the Padres.
Diamondbacks: LHP Patrick Corbin (Tommy John surgery) made his third rehab start on Friday night, allowing two runs on four hits in six innings for Double-A Mobile. Corbin is expected to make one more rehab start before a possible call-up to the majors.
Padres: 2B Cory Spangenberg left the game in the fourth inning with a sprained left knee. ... LHP Cory Luebke threw 11 pitches in one perfect inning in a rehab appearance with Double-A San Antonio on Friday night. It was Luebke's fifth rehab outing as he attempts to come back from his second Tommy John surgery.
Diamondbacks: RHP Chase Anderson (3-2, 3.54 ERA) will attempt to rebound from his worst outing of the season in a 10-5 loss at Colorado on Tuesday. Anderson allowed eight runs on eight hits and three walks while giving up three home runs.
Padres: RHP Odrisamer Despaigne (3-5, 4.83) has had mixed success against Arizona. The righty beat the D-backs on April 14 with seven innings of one-run, two-hit pitching in a 5-1 win. But Despaigne allowed season highs of eight runs on 10 hits in five innings on May 7 at Arizona in an 11-0 loss.