What he had was good enough to get his 16th win, tying him for the major league lead and setting a Washington Nationals team record.
Gonzalez gave up seven hits and needed 110 pitches to get through 5 2/3 innings, but he didn't allow a run until the sixth and the Nationals got more than enough offense from Bryce Harper and Danny Espinosa for Gonzalez to notch the victory in a 5-2 win against the Mets.
"That wasn't pretty, but it was a win," Nationals manager Davey Johnson said. "He did all right, but not to his standards."
Johnson said Gonzalez was leaving pitches up in the strike zone, and the manager thought his pitcher was affected by a 2 hour, 26 minute rain delay that pushed back the start of the game. Gonzalez did get his sixth hit of the season on a fourth-inning single.
"I told him, 'Your hitting was better, but your pitching is going downhill,'" Johnson said.
Gonzalez (16-6) wouldn't admit to being troubled by the delay, despite giving up seven hits. He has won more games in a season than anyone else since the Nationals moved to Washington in 2005.
"It means a lot," he said. "This is a thank you to the bullpen, a thank you to the team, but we're not done yet. We've got to continue to keep playing and hopefully we stay that way and keep winning."
Harper had a home run and a triple, and Espinosa also homered as the Nationals won for the third time in their past four games. Tyler Clippard pitched a perfect ninth for his 27th save in 31 chances.
Washington (75-46) has the best record in the majors and a five-game lead in the National League East over the Atlanta Braves, who lost 5-0 to the Dodgers on Sunday. The Nationals host the Braves in a three-game series starting Monday.
"It's going to be a lot of fun going into this series," Harper said. "Good for baseball, good for us and good for this town."
Jeremy Hefner (2-5) gave up five runs and eight hits as the Mets lost for the ninth time in 13 games.
"We're not exactly playing great right now," New York manager Terry Collins said.
Espinosa hit a two-run home run, his 14th, into the left-field visitors' bullpen to give the Nationals a 2-0 lead in the second inning.
It was Harper's team-leading sixth triple, and the 19-year-old added another run when he led off the fifth with his 12th homer off the front of the upper deck in right-center field, extending Washington's lead to 5-0.
"I think he was trying to send a message to me, 'Don't bench me,'" said Johnson, who held Harper out of the starting lineup Saturday. "He crushed that ball today."
New York was 1 for 11 with runners in scoring position, with the lone hit coming on Kelly Shoppach's run-scoring single in the eighth.
"It's part of a pattern," Collins said. "We had a lot of guys on. We had plenty of opportunities, but just couldn't get a big hit when we needed it."
The Nationals took two of three from the Mets and are now looking forward to extending their lead against Atlanta.
"We have a great team, but the Braves have been playing unbelievable baseball as well," Espinosa said. "It's not going to be an easy three games, it's definitely going to be a dogfight with them."
Shoppach, who was traded to New York from Boston last week denied that he had any part in text messages that reportedly undermined Boston Red Sox manager Bobby Valentine. The New York Daily News reported that Shoppach sent text messages using the phone of Red Sox first baseman Adrian Gonzalez. "I wasn't behind any texts," Shoppach said. ... Mets IF Daniel Murphy was ejected after being called out on strikes as a pinch-hitter to end the eighth inning. ... Nationals SS Ian Desmond was in the starting lineup even though manager Davey Johnson had said Saturday he would give Desmond the day off. Desmond went 0 for 4. ... New York opens a four-game home series with Colorado on Monday. RHP R.A. Dickey (15-4) faces the Rockies' RHP Alex White (2-6). ... Washington RHP Jordan Zimmermann (9-7) will start Monday against Atlanta RHP Tim Hudson (12-4).