Nationals starting pitcher Jordan Zimmermann leaves the mound in the seventh inning. (Jonathan Newton/WASHINGTON POST)

Jordan Zimmermann found trouble for the first time Tuesday night after his 100th pitch, and the Washington Nationals treated him like the elite starting pitcher they believe he will become. The go-ahead run stood on first base in the seventh inning. The Nationals wanted Zimmermann to remove himself from the bind, because that’s what the best starters do. They finish.

“He’s going to be in those situations a lot in his career,” pitching coach Steve McCatty said. “You got to learn to get through it.”

In the Nationals’ 2-0 loss to the Arizona Diamondbacks, Zimmermann again capped a brilliant outing with an ugly finish. After six scoreless innings, Zimmermann allowed a two-run home run and a double on his final two pitches. The Nationals’ offense gave Zimmermann no margin for error with its 13th shutout defeat this season, continuing a theme of under-supporting Zimmermann, who will make only one more start before he reaches his 160-inning limit and the Nationals shut him down for the season.

His performance this season, at 25, two years removed from Tommy John surgery, has made Zimmermann the Nationals’ best starting pitcher and their brightest development. But his recent penchant for unraveling at the end has provided him a final hurdle between being one of baseball’s best young starters and one of the leagues’ true aces.

“It’s definitely frustrating,” Zimmermann said. “It happened a couple times this year where it’s just one pitch at the end of the game. . . . I feel like I’m focused. I’m doing everything I can out there. It always seems like it’s something with me — towards the end of the game, something always goes wrong.”

Nationals fans waited outside the stadium as officials inspected the stadium for damage from the earthquake that shook the region. (Jonathan Newton/WASHINGTON POST)

Until Zimmermann takes the mound again, he will have to think about how Tuesday night’s start ended. He had dominated the Diamondbacks for six innings, striking out four, allowing just three hits, a walk and a hit batter that sparked momentary drama. His biting sliders and 94-mph fastballs overwhelmed Diamondbacks hitters. When he recorded the first out of the seventh inning, his ERA for the season had dropped to 2.99.

“He was throwing hard,” Manager Davey Johnson said. “He was making it look easy.”

And then he crumbled. He walked Chris Young, ball four coming on his 107th pitch. In his last start, against the Cincinnati Reds, Johnson had come to the mound and taken the ball with two outs and men on first and third. “Don’t make me have to come out there when you’ve got unfinished business,” Johnson had told him then. “You’re too good a pitcher.”

So with a man on first, even as Zimmermann’s pitch count matched his highest total this season, Johnson kept him in the game. He threw one pitch to bench player Sean Burroughs, a one-time top prospect who had battled substance abuse and had not hit a home run since 2005.

Catcher Wilson Ramos called for a fastball, low and away. Zimmermann zipped it 92 mph. “Right down the middle,” Ramos said.

There was no doubt from the moment Burroughs swung. He sent the ball into the right field seats, breaking the scoreless tie, putting the Diamondbacks ahead, 2-0. When Diamondbacks starting pitcher Ian Kennedy followed with a double to right, Johnson pulled Zimmermann for Tyler Clippard.

Zimmermann’s bitter conclusion recalled the implosion at the end of another otherwise stellar start. On Aug. 11, Zimmermann pitched into the seventh inning of a 1-1 game against the Cubs. After two quick outs, Zimmermann yielded a single and then consecutive home runs.

Nationals first baseman Michael Morse is hit by a pitch by Diamondbacks starting pitcher Ian Kennedy. (Jonathan Newton/WASHINGTON POST)

“It’s extremely important for your top-end guys that they get through those things,” McCatty said. “To me, he was cruising. You got to let guys go out there and learn how to get through these. And he’s going to do that. He. Will. Do that.”

Tuesday’s start shared something else in common with the unraveling in Chicago: the Nationals’ uncanny inability to score runs when Zimmermann pitches. The Nationals have scored 3.3 runs per game on days Zimmermann starts, one reason he does not deserve his 8-11 record. Six of those losses, Zimmermann has allowed less than two runs.

“Sometimes, it just makes it like you got to be perfect,” Zimmermann said. “If they get runs early, then you can settle in and not have to be so perfect. But it’s baseball.”

The Nationals’ best two chances to score off Kennedy came in consecutive innings, the fourth and fifth, when the Nationals stranded men on second and third and then left the bases loaded. Laynce Nix struck out in the fourth with both Ryan Zimmerman and Michael Morse in scoring position.

In the fifth, Zimmermann struck out looking at a curveball on the outside corner with the bases loaded and one out. Morse followed with an unusual at-bat. He checked his swing an inside pitch with the count 0-1, and the ball hit him . . . somewhere.

Morse insisted the ball had grazed his arm. Home plate umpire Marvin Hudson ruled it had hit the knob of his bat. Johnson argued that Morse wraps his hand around the knob, and the pitch had hit both — “To me,” Johnson said, “that’s getting hit in the hand.” On the next pitch, Morse struck out and the inning ended.

The Nationals’ loss included simmering bad blood. In the fourth inning, Zimmermann drilled Justin Upton in the left arm with a 94-mph fastball. The Nationals had hit Upton four times during their June series in Arizona, and his fifth hit by pitch against the Nationals did not sit well. Upton slammed his bat to the ground and barked at the mound as he went to first base. Two innings later, Upton, a National League MVP candidate, left the game.

In the bottom half, Kennedy hit Morse with an 89-mph sinker in the hands. As Morse doubled over and hopped out of the batter’s box, Hudson issued warnings to both benches. The teams heeded the warning and hit no more batters.

“Neither pitcher in my estimation was purposely trying to hit him. They’re trying to pitch them in. I thought Upton was reacting rather poorly. . . . He’s just trying to pitch him. I thought Upton overreacted to that one.”

Zimmermann’s start left him at 157 innings this season, three shy of the limit the Nationals prescribed for him at the start of the Nationals season. They will let him make one more full start, no matter how many innings, no restrictions. His primary task, the only one that has hurt him this season, will be finishing it.

“He’s a great competitor,” McCatty said. “I know that he’s disappointed and upset. Guys that are like that get through it, because they don’t quit. It’s a painful learning experience, but we’ve all been through it.”