The postgame trouble in the dugout made it clear, however, that the Braves still have plenty to play for in the regular season.
Johnson made a headfirst dive into first base but was thrown out by shortstop Jimmy Rollins to end the game, then argued with Pendleton after the Braves lost to Philadelphia 5-4 Saturday night.
Pendleton grabbed Johnson's jersey with two hands and pulled him face-to-face. There were angry words before they were separated.
There were suggestions the coach was irritated because Johnson threw his helmet in the dugout and it hit Pendleton. But Johnson wouldn't talk about the incident and Pendleton wasn't available.
"Rollins not only made a great play stopping that ball from going into the outfield, but to get up and through Chris out," Braves manager Fredi Gonzalez said.
The loss dropped Atlanta one game behind St. Louis for the best record in the National League. If they're tied following Sunday's season finale, the Braves will get home-field advantage throughout the NL playoffs.
"That's still a big carrot for us, for us to win and St. Louis to lose to get the No. 1 seed," Gonzalez said.
Down 5-1, the Braves rallied in the ninth on Justin Upton's three-run homer, his 27th, with two outs. Freddie Freeman singled and Evan Gattis walked to keep the rally going against Jonathan Papelbon.
Johnson hit a grounder to the hole and Phillies shortstop Jimmy Rollins made a diving stop, got up and made a one-hop throw to first baseman Darin Ruf for the final out.
"Heck of a play to end the game," Phillies manager Ryne Sandberg said. "My first thought was he was going to ... third base because it was right in front of us. But when I saw him go ahead and go to first, a perfect one-hop throw and got him. Outstanding!"
Mike Minor (13-9) took the loss after allowing two earned runs in six innings.
Philadelphia rookie Ethan Martin started and allowed a first-inning run in three innings. Fellow rookie Luis Garcia (1-1) pitched two innings of scoreless relief to pick up the win.
Eliminated from playoff contention a while back, the Phillies started five rookies. Cesar Hernandez had a career-high four hits and scored twice, and Cameron Rupp hit a two-run single.
"He's got a knack for swinging the bat," Sandberg said of Hernandez. "He's got good hands. He hits. He hits the fastball."
The NL East champion Braves committed two of their three errors in the seventh as Philadelphia added two runs with the help of a wild pitch by reliever Jordan Walden.
Hernandez put a bunt down the first-base line on the game's first pitch for a single, and Rollins followed with a double on the second pitch by Minor. They scored on Rupp's single.
The Braves scored in the first on singles by Jason Heyward and Upton and a sacrifice fly by Freeman.
The Phillies held the 2-1 lead until the seventh, at which they looked like the team heading to the postseason and Braves looked anything but.
Hernandez opened with a single and took second on Walden's wild pitch. Rollins singled again and Hernandez was initially held up at third, only to restart and scored when Gattis, a converted catcher, bobbled the ball in left.
Rollins took third when Walden's pickoff throw sailed past Freeman at first base and toward the right-field corner. Domonic Brown's RBI single made it 4-1, and Philadelphia added a run in the eighth on Chase Utley's single.
The Braves made it close in the ninth when second baseman Elliot Johnson reached on a one-out single, pinch-hitter Jose Constanza followed with a single and Upton homered with two outs.