HOUSTON — James Paxton had only allowed one run when manager Aaron Boone motioned to the bullpen to summon Chad Green in the bottom of the third in Game 2 of the ALCS.

Paxton, who started Game 1 of the ALDS for the Yankees against Minnesota, and pitched as well as anyone in the league for much of the second half of the season, had a succinct reaction when he saw his manager coming to get him: “Crap.”

It was Paxton’s second straight shaky postseason start. He gave up four hits in 2¹/₃ innings to put the Yankees in a 1-0 hole to the Astros before the bullpen took over at Minute Maid Park in what became a 3-2, 11-inning loss Sunday to even the series at one game each.

“I just felt like we were covered as far as today with getting some length and having guys rested,’’ Boone said afterward. “Obviously going into an off day [Monday], we’re just going to be aggressive. I thought he was struggling with his command. And it ends up — it doesn’t end well.”

It forced the Yankees to tax their bullpen — something they could afford to do after Masahiro Tanaka’s strong start in Game 1 and with no game Monday.

Paxton ran into trouble in the bottom of the second when he allowed a leadoff single to Alex Bregman and a walk to Yordan Alvarez. Yuli Gurriel’s fly ball to right moved Bregman to third, and he scored on Carlos Correa’s double down the left-field line to give Houston a 1-0 lead, their first of the series.

Paxton righted himself against the two worst hitters in the Astros’ lineup, fanning Robinson Chirinos, then Jake Marisnick to get out of the inning without further damage.

But Paxton had issues again in the third, after striking out George Springer to open the inning. A Michael Brantley flare single to right and a lined single to left by Jose Altuve got Boone to go to Green, who retired Bregman and Alvarez to end the inning.

The brief outing followed Paxton’s playoff debut in the ALDS, when he gave up three runs in 4²/₃ innings in a Game 1 win over Minnesota.

And it was Paxton’s second rough start of the year in Houston, where he allowed five runs in four innings in an April 10 loss. It was Paxton’s third start as a Yankee, and afterward, special adviser Carlos Beltran showed Paxton how he was tipping some of his pitches.

Paxton and Boone were confident he wasn’t tipping his pitches on Sunday, though Fox cameras during the game showed Bregman telling his teammates “glove” during the game.

“I don’t think they were getting anything,’’ Paxton said.

He was more upset about his lack of command — as was Gary Sanchez.

“He had to make a lot of pitches tonight,’’ Sanchez said through an interpreter. “The command wasn’t where we wanted it to be. It happens. I look forward to the next time. Hopefully he does a better job the next time.’’

And it’s why Paxton understood the move to yank him early.

“It’s not about me,’’ Paxton said. “It’s about the team and I’m totally on board with that. If they want to take the ball away, they will. We’re trying to win ballgames and it’s different in the postseason with a rested pen.”

He added he’d be ready if the Yankees call on him again before his next scheduled start.

“I’ll be ready to go,’’ Paxton said.