The Padres' Tommy Medica homered in the fourth to tie the score 2-2. It was Medica's third homer since being elevated from Double-A on Sept. 10.
Medica's blast erased Kennedy's mistake in the top of that inning, one that came without him delivering a pitch.
Paul Goldschmidt opened with a double and advanced to third on Martin Prado's single. With runners at the corners, Kennedy stepped toward third on a pick-off attempt, but didn't throw the ball. Goldschmidt scored on the balk for a 2-1 lead.
"I missed the sign," Kennedy said.
The Diamondbacks had pulled even at 1 in the third when Delgado drove in Gerardo Parra with a single up the middle. Parra led off the inning with a double after Kennedy retired the first six batters.
Two doubles got the Padres a run in the first. Headley's double off Parra's glove in right-center chased home Denorfia, who was aboard after his one-out double.
Rene Rivera, Headley and Denorfia all had three hits for the Padres.
But what stood out to the Diamondbacks was Kennedy's standout peformance.
"He made a lot of good pitches," Montero said.
NOTES: Venable isn't 100 percent with his abdominal strain, but he returned to the starting lineup. Venable, who has a team-high 22 HRs, missed two games. ... SS Ronny Cedeno, who was beaned by a pitch from Heath Bell on Monday, remains out with a headache. ... Goldschmidt extended his hitting streak to 15 games with a fourth-inning double. ... Diamondbacks RHP Trevor Cahill (8-10) starts in Thursday's series finale. He's 5-0 with a 2.64 ERA since returning from a hip contusion on Aug. 17.