PITTSBURGH — For a second straight start, Jordan Montgomery didn’t have full command of his four-pitch arsenal.

The rookie lefthander nonetheless turned in his best outing in three starts, producing six strong innings Sunday in the Yankees’ 2-1 loss to the Pirates in front of 27,840 at PNC Park.

“I never expect to have everything, but I didn’t really have much going today at all,” Montgomery said. “Just tried to battle and keep us in it.”

He did, but it was not enough as the player who previously wore Montgomery’s No. 47 with the Yankees continued a masterful start to the season.

Showing an effective sinker and darting curveball the Yankees frequently saw when times were good, Pirates righthander Ivan Nova mostly shut down his former team. He allowed one run, four hits and a walk in seven innings in improving to 2-2 with a 2.00 ERA.

“I thought we hit the ball better than probably the amount of hits we had today,” Joe Girardi said of how the Yankees fared against Nova. “I thought he used his fastball up and down and he used his breaking ball pretty effectively.”

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Girardi, as you might expect, was much more interested in talking about his own pitcher, who allowed two runs and seven hits in six innings. Montgomery, 24, fell to 1-1 but lowered his ERA from 4.22 to 3.78.

“It’s really encouraging,” Girardi said. “I think it’s a pretty big step so far for a pitcher at this level, not to have all your stuff and to be able to minimize damage. That says something about him. You want him to keep taking steps forward and I thought he took another one today.”

Montgomery, though not pleased with the result, remained confident.

“I mean, if you can go six innings, two runs with nothing, obviously I deserve to be here,” he said. “So I want to be better and pitch with my strengths and just win.”

The Yankees (11-7), who lost two of three to the Pirates (8-10), are off Monday before starting a three-game series at Fenway Park on Tuesday night.

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The Yankees, who got on the board in the seventh when Jacoby Ellsbury hit a hanging curveball from Nova for his second homer of the season to make it 2-1, nearly took Montgomery off the hook for the loss in the later innings.

Aaron Judge singled with one out in the ninth against Pirates closer Tony Watson and pinch hitter Matt Holliday walked. Ronald Torreyes grounded to second for what looked like a surefire game-ending double play, but second baseman Josh Harrison butchered it — not a surprise in that the Pirates kicked the ball around the field all series (six errors) — to load the bases.

Watson rebounded to strike out Aaron Hicks and, after falling behind Pete Kozma 2-and-0, got him to hit into a 5-4 forceout to end it. Watson recorded his sixth save in six chances.

“The whole approach was to get something out over the plate and drive it somewhere,” Hicks said, “and I didn’t do it.”

The Yankees, who went 0-for-6 with runners in scoring position and stranded eight, put two on with one out in the eighth against Daniel Hudson. Then Chase Headley popped out and — after a wild pitch put runners on first and third — Starlin Castro lost a nine-pitch battle, fanning on a 95-mph fastball.

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The Pirates, who got a sacrifice fly from David Freese in the first and an RBI double from Gregory Polanco in the third, didn’t distinguish themselves either, going 1-for-10 with runners in scoring position and stranding 10. They loaded the bases with none out in the first against Montgomery and did it again in the seventh against Bryan Mitchell but managed a total of only one run.

“I thought our pitching staff did a really good job of minimizing damage,” Headley said. “Felt like we were in trouble all day, but they found ways to get us out of innings and gave us a chance. We had some chances and just weren’t able to do it.”