The left-hander said he "took a couple of steps back" Sunday in an otherwise impressive season for the Miami-area native.
Gonzalez gave up five runs in the first inning and six overall while going 4 1/3 innings as the Pittsburgh Pirates beat the Nationals 11-8 with 14 hits, seven coming with runners in scoring position.
Washington manager Dusty Baker said Gonzalez was a little under the weather before he took part in the longest nine-inning game (4:24) in the history of both teams.
"I didn't want Dusty to say that. That is not an excuse," said Gonzalez, whose ERA rose to 2.96. "It is self-explanatory the way the game ended. It was a head scratcher."
The Pirates won the last two games of the four-game set.
"It was crazy from the start to finish," said Clint Hurdle, the Pirates manager. "I just didn't know when (it would end). Both teams had guys up in the bullpen in the first inning."
It was not all bad news for the Nationals, as Baker was able to remove several starters during the game as the fans applauded. That included first baseman Ryan Zimmerman, second baseman Daniel Murphy, third baseman Anthony Rendon, right fielder Bryce Harper and left fielder Jayson Werth, who came off to start the top of the ninth in what may have been his last regular-season game with Washington.
"The fans were into it. That was the nice thing about today's game," Gonzalez said.
Max Moroff delivered a bases-loaded double in the first inning and walked with the sacks full in the eighth for the Pirates.
Jacob Stallings added three run-scoring hits for Pittsburgh.
The Nationals (97-65) failed to set a franchise record for wins in a season but will take the second-best record in the league into their home game Friday in the opener of the National League Division Series against the Chicago Cubs.
The Pirates (75-87) finished with a losing record for the second year in a row.
Pittsburgh scored five times in the top of the first.
The first run came as Jordan Luplow was hit by a pitch with the bases loaded. Moroff followed with a three-run double down the left field line. Stallings, the No. 8 hitter, came up next and had a run-scoring double to make it 5-0.
Rendon hit a three-run homer in the last of the first off Steven Brault to trim the margin to 5-3. That gave Rendon 100 RBIs on the year, and he finished with 25 homers.
In the third, Werth hit his 300th career double to drive in a run in third to trim the margin to 5-4.
Pittsburgh's David Freese had an RBI single in the fifth to make it 6-4 and end the day for Gonzalez (15-9).
Stallings had another RBI double in the sixth off Tanner Roark, and Starling Marte drove in a run with a fielder's choice for an 8-4 lead.
Washington's Michael A. Taylor hit a solo homer to lead off the seventh to cut the deficit to 8-5. It was the 19th homer of the year for Taylor. Adrian Sanchez (2-for-3) had an RBI double to make it 8-6.
However, the Pirates' Josh Bell hit an RBI single in the eighth for a 9-6 lead off Oliver Perez, and the walk by Moroff made it 10-6. Stallings drove in a run with an infield single for an 11-6 edge.
"He has shown a lot of growth," Hurdle said of Bell, who ended the year with 26 homers. "The future is bright."
Angel Sanchez (1-0) allowed no runs in two innings and got his first big league victory.
The Nationals scored two unearned runs in the ninth with two outs before George Kontos got the last out for his first save of the year.
"He looked better," Baker said of Harper, who entered the game 1-for-14 since Tuesday when he came off the disabled list. "He is laying off bad pitches."
NOTES: Pittsburgh CF Andrew McCutchen, the subject of trade rumors last winter, was lifted for a pinch runner after he doubled in the fifth. He finished the year with 28 homers and 88 RBIs. ... Washington 1B Ryan Zimmerman, who had a career-high 36 homers this year, was taken out for 1B Adam Lind at the start of the top of the fourth to a round of applause. ... GM Neal Huntington said before the game that if the Pirates keep McCutchen it would be to play center field. He also said he expects all members of the coaching staff to return. ... Washington RHP Max Scherzer, who left his start in the fourth inning Saturday with a hamstring issue, said he hopes to be ready for the playoffs but did not guarantee he would be ready to start Game 1.