Kimbrel, who hasn't walked more than 26 batters in any of the last three seasons, walked two during the 11th inning and later allowed the game-winning hit, a single to left through a five-man infield to the Cubs' Starlin Castro.
Kimbrel was left to lament the absence of his breaking ball and a few close pitches that didn't go his way in that final inning when he loaded the bases on a one-out walk to Anthony Rizzo, who stole second base, an infield single to Kris Bryant and then another walk, this time to pinch-hitter David Ross.
"Everything was kind of all over the place today," Kimbrel said. "… A few pitches I thought were pretty close, I didn't get the call. My breaking ball … when I can't throw that for a strike, guys can sit on one pitch.
"The team needed to me to go out there and throw a scoreless inning so we can come back in and score, and I didn't do that."
This was Kimbrel's first loss since Aug. 2, 2014, which, oddly enough, came against the Padres when he was still a member of the Braves.
From the dugout, manager Bud Black thought that Kimbrel didn't miss by much a few times during the walks.
"He couldn't quite get the curveball in the zone. He was keeping the ball down. [He] made some pitches that looked close from the dugout," Black said.
Aside from missing the command on his breaking ball, Kimbrel was most upset about not being able to give the Padres, who tied the game with four runs in the ninth inning, another chance to push across the go-ahead run.
"The guys did a heck of a job that last inning to come out and score those runs. I felt like we did well," he said. "I just didn't do my job today."
Corey Brock is a reporter for MLB.com. Keep track of @FollowThePadres on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.