It was the second straight loss for Strop, who also gave up two runs in a 6-5 loss to the Cardinals on July 8.
''The stuff is there,'' Strop said. ''I feel good; nothing's hurting. ... It's not going my way right now.''
Cubs manager Joe Maddon said he remains confident in Strop.
''It's so strange,'' Maddon said. ''I really have faith in this guy. I really believe he's that good. He let it get away from him but I still believe he's one of the best. We've just got to continue to work him through this moment.''
Schwarber, the left-handed hitting rookie, had two singles and a double - all to right field - in his first start at catcher after being recalled earlier in the day because of catcher Miguel Montero's thumb injury. He also had a throwing error.
''I felt good back there,'' Schwarber said. ''I had that one get away from me, but it's going to happen sometimes. It's part of the game. But I felt like I received the ball good back there.''
The rookie's first call-up to the majors lasted only six days, when he made five starts as the designated hitter. This time, he's back and will have at least a share of the starting job at catcher.
Schwarber's recall came only five days after he was named the MVP of the All-Futures Game on Sunday.
Kyle Hendricks took a streak of 22 1/3 scoreless innings into the game before giving up a first-inning run. Schwarber's throwing error on a stolen base by Nick Markakis set up Johnson's run-scoring single to right field.
Hendricks, who allowed two runs, one earned, in 5 2/3 innings, said Schwarber was ''awesome'' and ''very mature for a 22-year-old kid.''
The Cubs couldn't take advantage of having runners on first and third with no outs in the first. They again had runners on first and third in the third. Following Kris Bryant's second strikeout, Anthony Rizzo walked to load the bases. Jorge Soler followed with a two-run single to center field.
Braves right-hander Julio Teheran allowed two runs and five hits and three walks in 4 2/3 innings.
Atlanta's bullpen combined for 4 1/3 scoreless innings. Arodys Vizcaino (1-0) pitched a perfect eighth, and Jim Johnson earned his sixth save with three straight outs in the ninth. Johnson has moved into the closer's role following Jason Grilli's season-ending Achilles injury.
Ryan Kelly, who was recalled from Gwinnett before the game, gave up one hit in a scoreless sixth.
Pinch-hitter Jonny Gomes was called safe at first in the fifth before the call was overturned following a review that lasted only 40 seconds. Shortstop Starlin Castro bobbled Gomes' grounder before throwing to first.
Cubs: Montero is expected to be out longer than two weeks with a left thumb sprain. Montero was expected to see a hand specialist in Chicago on Friday and to be checked again in Arizona this weekend.
Braves: 1B Freddie Freeman (right wrist contusion), on the DL since June 23, retroactive to June 18, could begin his injury rehab Sunday or Monday.
Cubs: LHP Jon Lester (4-8) will try for his first win since May 16 when he makes his fifth career start against the Braves. He is 0-6 since a 4-2 start.
Braves: Rookie LHP Manny Banuelos (1-0), who has allowed only one run in his first 12 innings, will make his third start.