Even with Jacob deGrom not at his dominant best, he still matched the all-time MLB record with his 39th consecutive start in which he allowed three earned runs or fewer.

Of course, the two-time Cy Young winner now has earned a win in fewer than half of those outings.

The first-place Mets have totaled three runs in losing the first two of a three-game series against their latest out-of-it opponent, and they heard several rounds of boos throughout a 4-1 loss Tuesday night to the Cubs at Citi Field that dropped their NL East lead to just a half-game.

“It’s a few rough games, but we’ll be OK,” said deGrom, who worked six innings of three-run ball. “We went to Pittsburgh and lost the first one and ended up winning the series. We need to take the game [Wednesday] and prepare for the next one.

“These guys do a good job of flushing it and getting ready to play, so I think we’ll be fine.”

DeGrom allowed three runs on four hits, with zero walks and 10 strikeouts, over a season-high 96 pitches. In doing so, he matched baseball’s all-time record, set by White Sox pitcher Jim Scott (1913-14), of 39 consecutive starts allowing three earned runs or fewer.

The $137.5 million righty is 19-6 with 14 no-decisions during his record-tying stretch.

“I just didn’t make some pitches when I needed to in the [two-run] fourth [inning] and I wasn’t able to execute when I need to,” said deGrom, who also allowed a solo homer to Ian Happ in the second inning. “I needed to go out there and put up zeroes and wasn’t able to do it. Tonight’s on me.”

That was hardly the case.

Pete Alonso ripped a solo homer in the ninth inning to prevent the Mets (89-54) from getting shut out for the eighth time this season — after they managed two runs Monday in the series opener.

“We just didn’t mount much offensively, had a lot of fly balls that weren’t hit deep enough and when we did hit a ball, they caught it,” Mets manager Buck Showalter said. “We pitched well enough to be in the game more.”

The Mets thought they had scored twice in the first inning, but Alonso’s would-be home run down the left-field line was ruled foul and upheld via video review. Alonso slammed his bat and had words with Cubs starter Adrian Sampson (six scoreless innings) after he subsequently was walked.

“I wasn’t upset that he didn’t throw the ball over the plate, I was frustrated the ball [in the corner] went foul,” Alonso said. “It’s about putting runs on the board, and I was just frustrated at that.”

There were other frustrating moments, to be sure. Jeff McNeil had been credited with a single earlier in the first inning when his grounder clipped baserunner Brandon Nimmo before getting into right field.

McNeil also stroked a two-out single in the third inning, sending Nimmo from first to third. But Sampson got Alonso to tap his first offering to shortstop for a force play to end the inning.

The Cubs plated two runs in the fourth on a sacrifice fly and a safety squeeze. Franmil Reyes and Happ opened the inning with singles against deGrom. Pinch-hitter Michael Hermosillo attempted to sacrifice bunt, but catcher James McCann’s throw to first clipped him on the helmet to load the bases.

Showalter argued that Hermosillo was inside the first-base line when the ball struck him, but the play was not reviewable. Yan Gomes followed with a sacrifice fly to right. Happ then beat Alonso’s throw home on Patrick Wisdom’s bunt for a three-run Chicago lead.

Seth Lugo replaced deGrom in the seventh inning and surrendered a two-out homer to No. 9 hitter David Bote for a four-run lead the Mets could not overcome.

“First inning, we get a firm-hit ball that Nim just couldn’t get out of the way, and Pete’s ball misses by inches,” Showalter said. “That’s kind of the way it was going tonight.

“I’ve said many times that finishing off a good season is really challenging. It’s challenging because you see the finish line and you’re trying to get there, and sometimes get away from the things that got you there. And the other team sometimes doesn’t cooperate.”