One of the Yankees’ feel-good stories of the year has been cut short.

Manny Bañuelos was designated for assignment on Tuesday to make room on the roster for JP Sears, who was called up from Triple-A to make a spot start against the Athletics.

Bañuelos, the former top pitching prospect who finally earned his way to The Bronx this season, was the odd man out in the bullpen after posting a 2.16 ERA across four games in pinstripes.

“Difficult,” manager Aaron Boone said before the Yankees’ 2-1 win over the A’s at the Stadium. “Obviously a numbers game, a crunch. One of the things that made it difficult, on top of who the person is and the story and how much it’s been a joy to be around him every day … is [that] we really think he can pitch.”

But the left-handed Bañuelos was used sparingly, as protection for length for a team that hasn’t needed it very often. Since being called up on May 26, he pitched just 8 ¹/₃ innings, making him the choice to go instead of another reliever, such as Ron Marinaccio, who has minor league options remaining, but has posted 10 straight scoreless outings over the last month-plus.

Bañuelos, who did not have any minor league options left, will go on waivers, allowing other teams to potentially claim him and add him to their 40-man roster.

“Certainly hope the best for Manny and selfishly I hope he remains with us, but I certainly understand the situation and the process too,” Boone said.

Aroldis Chapman (Achilles) made the third and likely final appearance of his rehab assignment Tuesday, tossing a perfect inning with two strikeouts for Triple-A Scranton/Wilkes-Barre. He is expected to be activated off the injured list in the next few days.

Domingo German (shoulder) also made the second start of his rehab assignment with Double-A Somerset, throwing 43 pitches over 3 ¹/₃ scoreless innings.

Gleyber Torres remained out for the second straight game after getting a cortisone shot on his inflamed right wrist, but he hopes to be back by Thursday against the Astros.

Torres was already feeling some improvement on Tuesday after playing through the wrist soreness for about three weeks, he said.

“I don’t want to [make] excuses,” Torres said. “But I feel it every swing. I just tried to work on that, don’t put too much attention on the pain. But the last couple days, getting pretty sore. … I don’t want to put too much pressure on it and maybe get a worse injury for long[er].”

Torres, who had been wearing tape on the wrist and getting physical therapy, said it was important for him to play through series against the Rays, Blue Jays and Astros before addressing the wrist.

As for the ankle he sprained on Sunday, Torres said it was still sore Monday but felt “fine” Tuesday.

Aaron Judge told reporters he did not call himself “the best player on the team” Sunday in a postgame interview with YES Network — at least he didn’t mean to.

Judge explained that he was trying to say, “best team on the planet,” which he said came out as “best planet on the team.”

Isiah Kiner-Falefa (bruised finger) and Anthony Rizzo (hit by pitch on right elbow) were both in the lineup Tuesday. … Joey Gallo went 0-for-3 with two strikeouts as his skid reached 0-for-24, with 13 strikeouts and four walks, over his past nine games.