Gonzalez scolded Braves fans for littering the field and putting players and umpires in danger.
"I think we have very passionate fans here in Atlanta, and I think I'm a little disappointed with the reaction of throwing bottles and beer cans and you name it," Gonzalez said. "For me, that's uncalled for.
"I understand the disappointment. But we can't do that. As Atlanta Braves and people from Georgia, it doesn't look good, and I'm a little disappointed in our fans from that point. You get people injured out there."
It was the same type of ending as last year, but different.
Last season, the Braves led St. Louis by 10½ games in the wild-card race before play on Aug. 26 and still were up by 8½ games on the morning of Sept. 6. Atlanta went 9-18 in September, ended with a five-game losing streak and finished a game behind the Cardinals, who went on to win the World Series.
This year, with a second wild card added, the Braves went 94-68 and the Cardinals 88-74, setting up the wild-card matchup in the expanded postseason.
Atlanta then played one of its worst games of the year, blowing a two-run lead, making three errors that led to four unearned runs and going 1 for 8 with runners in scoring position. The Braves had the fewest errors in the NL during the regular season.
One of the errors was by Jones, whose bad throw on a potential double-play grounder helped allow the Cardinals to score three runs in the third and go ahead for good. Second baseman Dan Uggla and shortstop Andrelton Simmons also made throwing errors in the seventh, helping the Cardinals add two runs.
The 40-year-old Jones was 1 for 5, reaching on an infield single in the ninth and ending his career stranded at third base when Uggla hit a game-ending groundout. Jones tipped his helmet before his final at-bat.
"I walk out of here knowing that I brought it every single day," Jones said. "When you know that, it makes it easier to walk away."
Even after the controversial call, Atlanta had a chance in the eighth. The Cardinals brought in closer Jason Motte, who loaded the bases with a walk to pinch-hitter Brian McCann before striking out Michael Bourn on a 3-2 pitch.
Atlanta had won a record 23 straight starts by Medlen, who was 9-0 with a 0.97 ERA in 12 starts this season. He had not lost as a starter since May 23, 2010, at Pittsburgh. In this one he allowed five runs — two earned — and three hits in 6 1-3 innings.
David Ross' two-run homer put the Braves ahead in the second, but after Jones' error the Cardinals went ahead on an RBI double by World Series star Allen Craig, Yadier Molina's run-scoring groundout and David Freese's sacrifice fly. Holliday homered in the sixth to make it 4-2.
After Uggla's error on Freese's leadoff grounder in the seventh, Simmons made his bad throw on a grounder by rookie Pete Kozma and Matt Carpenter hit a run-scoring infield single to the pitcher.
Bourn's RBI grounder in the seventh was the only other run the Braves could muster. Atlanta sent the tying run to the plate in the seventh, eighth and ninth innings.
And now the Braves have all winter to think about another season with a sour ending.