Johnson, who pinch-hit in the eighth for second baseman Diory Hernandez and remained in the game, drove a 1-1 pitch a couple of rows behind the short fence in the right-field corner for his eighth home run after a one-out walk to Adam LaRoche.
"I know sometimes he'll go with the changeup, so I kept it in the back of my mind and kept myself back," Johnson said. "At that point of the game, you're looking for a break. But you make your own breaks."
It was the fifth homer allowed this season by Mota (3-3), making his second appearance since last Tuesday's well-documented dust-up with Milwaukee slugger Prince Fielder.
Rookie Kris Medlen (3-3) pitched two hitless innings for the win, striking out four and walking one. The right-hander fanned Andre Ethier, Manny Ramirez and Matt Kemp in the eighth after a leadoff walk to Rafael Furcal. In 16 relief appearances this season, Medlen has 29 strikeouts in 27 2/3 innings.
Rafael Soriano, who served up Ethier's three-run walkoff homer in Thursday's series opener, got three outs for his 17th save in 19 attempts despite giving up an RBI double to Ethier in the 10th.
After an intentional walk to Ramirez, the right-hander retired Kemp on a grounder to shortstop Yunel Escobar -- who robbed him of a tying RBI single with a fully-extended diving play toward the middle and threw him out.
"My first thought was to make sure the ball didn't go through," Escobar said through a translator. "I don't know if that was the best play I've made, but it was the most important."
Dodgers left-hander Clayton Kershaw and Braves 34-year-old rookie Kanshin Kawakami matched zeros through seven innings in a matchup of pitchers facing their respective opponents for the first time. Kawakami made 125 pitches, scattering four singles and striking out four. Kershaw threw 104 pitches, allowing two hits and striking out 10.
"Kershaw took care of what he could control," manager Joe Torre said. "After his last outing, he became very determined -- not that he wasn't determined the last outing, but this kid has a lot of heart. And certainly, you know his ability."
Kershaw struck out 10 of his first 18 batters, retiring 20 of 22 after Ryan Church opened the game with a double into the left field corner. Atlanta's only other hit against the 21-year-old right-hander was a one-out single in the fourth by Garret Anderson. The only walk Kershaw allowed was to Escobar, whom he picked off to end the seventh.
"He really deserves the victory, but you could say the same on the part of Kawakami," Ethier said. "We're frustrated to lose in extra innings, but just losing is the frustrating part."
Kawakami held the Dodgers to one hit over the first four innings before giving up singles to his first two batters in the fifth. A collision between second baseman Hernandez and right fielder Matt Diaz on a foul pop near the stands prolonged Brad Ausmus' at-bat, but lead runner Orlando Hudson was tagged out in a rundown as Kawakami fanned Ausmus, and Kershaw left Tony Abreu stranded at second with a groundout.
The Dodgers' best scoring chance against Kawakami came in the seventh when Kemp led off with a single, stole second and continued to third on a throwing error by former Dodgers catcher David Ross. Kawakami issued one-out walks to Hudson and Abreu, but came back to strike out Ausmus and Mark Loretta, who pinch-hit for Kershaw.
"We had our opportunities for sure," Kershaw said. "We're just in a stretch where we're not making that big pitch or getting that big hit. We're going to be fine, though."
Braves third baseman Chipper Jones missed his second straight game because of a strained oblique muscle on his left side, which occurred while he took batting practice on Friday. The Braves are 10-9 this season in games that he doesn't start.
Because of the Dodgers' 12-inning loss on Friday night and the Yankees' 15-inning win over Boston, Los Angeles entered Saturday not having the best record in the majors for the first time since May 2, when the team was 16-8. ... Ross' error was his first in 29 starts this season behind the plate. ... Kershaw is 6-1 with a 1.06 ERA in his last 10 starts beginning with a no-decision on June 16 -- the best ERA in the majors during that stretch.