Jacob deGrom walked off the mound shaking his head after completing Thursday’s sixth inning. It was the only one all night, of course, in which the perfectionist didn’t post a zero on the scoreboard.

The team co-ace’s fifth start since returning from the injured list was just as encouraging as the first four for the first-place Mets, who began a stretch of 20 of 23 games played against sub-.500 teams with a 3-1 win over the Rockies at Citi Field.

“Jake was great for us. Shocker,” Pete Alonso said after the Mets’ got back on track after two Subway Series losses earlier this week to the Yankees. “Jake was awesome for us, and it’s great to have him back.”

Working with two extra days of rest since his previous outing last Thursday, deGrom retired the first 12 batters he faced and departed with a 3-1 lead after six innings. The two-time Cy Young winner allowed one run on three hits with one walk and nine strikeouts over an 87-pitch effort, a handful shy of his season-high of 95 last week against the Braves.

“I feel good. We went a little bit above, in the one in Atlanta, and I felt good after that, too,” deGrom said. “I think that was the real test. What did I end up tonight, 87 [pitches]? So I think probably the next one probably it will be they’ll let me go however long, 100-plus.

“We’re checking off all the boxes and [moving] towards that.”

Alonso belted a two-run homer in support of deGrom, who improved to 3-1 with a 2.15 ERA over five starts since returning from the injured list this month.

“Sometimes when guys go on extra rest they aren’t quite as crisp command-wise, but he was the difference in the game for us,” Buck Showalter said after the Mets improved to 80-46. “The whole idea is to keep all of our pitchers around and healthy, not just Jake.”

Max Scherzer also missed nearly seven weeks bridging May and July with an oblique strain, and deGrom finally made it back to the rotation on Aug. 2 — after missing nearly 13 months with shoulder issues.

The 34-year-old deGrom opened Thursday’s outing with seven strikeouts among the first dozen batters he faced over four perfect frames.

The Mets had multiple base runners in two of the first three innings against Rockies righty Ryan Feltner, grabbing a 3-0 lead through three.

Tyler Naquin (2-for-4) snapped an 0-for-19 skid with a single for runners on the corners in the third, but rookie Brett Baty — who went 1-for-4 in his Citi Field debut — struck out looking for the third out.

Francisco Lindor and Alonso — each playing his 125th of the Mets’ first 126 games — combined to drive in all three runs in the third. After Lindor’s 85th RBI of the season came home on an infield out, Alonso crushed a 3-0 four-seam fastball from Feltner off the facing of the second deck in left-center for his team-best 31st homer of the year and a 3-0 lead.

The Rockies finally got their first two base runners against deGrom in the fifth, on an infield single by Jose Iglesias and a double inside third base by Randal Grichuk. But deGrom stranded both runners in scoring position with a punch-out of Sam Hilliard, his eighth of the game, and a fly-ball out by Brian Serven.

The Rockies finally got to deGrom on Ryan McMahon’s one-out solo blast into the visiting bullpen in the sixth, but the four-time All-Star completed the inning by whiffing Charlie Blackmon and getting C.J. Cron to bounce into a force play for the third out.

Asked if he hoped to stay in for the seventh, deGrom said, “I prefer going out there and finishing the inning, so where are you pushing it to? I think being around that same [pitch-count] spot a couple of times now, hopefully the next time we go out there for 100-plus.

Seth Lugo escaped a self-induced bases-loaded jam in the seventh and closer Edwin Diaz worked a scoreless eighth against the middle of the Rockies’ lineup before Adam Ottavino recorded the final three outs in the ninth for his first save of the season.