Clay Holmes of the New York Yankees reacts after surrendering...

Clay Holmes of the New York Yankees reacts after surrendering a two-run homer in the ninth as the Red Sox tied the score on Friday. Credit: Jim McIsaac

The Yankees had overcome a major baserunning flub that cost them a run, an injury, a pair of errors and a lackluster offense that generated three runs in an inning in which a ball never left the infield.

Somehow, they still had a two-run lead with no one on and two outs in the ninth against the Red Sox on Friday night at Yankee Stadium.

But Clay Holmes allowed a single and a tying home run, Tommy Kahnle gave up a go-ahead two-run homer on his second pitch of the 10th and the Red Sox went on to a 5-3 victory before a sellout crowd of 47,158.

The Yankees (54-36) have lost four in a row and 14 of 18.

Holmes, called in to protect a 3-1 lead, retired Rafael Devers and Connor Wong on routine grounders to begin the top of the ninth before giving up a pinch-hit single by former Met Dominic Smith. Holmes got ahead of Masataka Yoshida 0-and-2, but on the eighth pitch of his at-bat, Yoshida drove a 3-and-2 sinker 405 feet to rightfield for his third home run to tie the score. It was Holmes’ fifth blown save in 24 chances.

Ceddanne Rafaela led off the 10th with a 412-foot two-run homer to center off Kahnle, who in his previous 10 appearances hadn’t allowed a run in 8 1⁄3 innings, striking out 13.

“A tough one,” manager Aaron Boone said. “Obviously, especially considering what we’re going through right now, to have them take it and then pile on there in the extra frame. It’s a difficult time. You’ve got to dig down and a quick turnaround tomorrow. Get ready to play and find out what we’re made off a little bit. You’re going to be tested all the time, with tough spots in the season, which clearly we are right now. Obviously, extremely tough losses when you’re going through it, and this falls under that category.”

When Juan Soto began the bottom of the 10th with a line-drive single to right, ghost runner Ben Rice wound up at third after running most of the way to third, taking a few steps back toward second and turning around again. But with the crowd chanting ‘’MVP!’’ Aaron Judge fouled out to third baseman Devers on Kenley Jansen’s first pitch, Alex Verdugo popped to first on the first pitch and Oswaldo Cabrera — who had replaced an injured Gleyber Torres in the fourth — grounded to first to end it.

Yankees starter Nestor Cortes allowed one run, three hits and a walk in six innings, striking out eight in a 97-pitch gem. Cortes, who weathered a 38-minute rain delay before the bottom of the third, struck out the first two batters and the last two he faced.

Torres left the game for a pinch runner after beating out an infield single. The Yankees later announced that Torres left with a tight right groin, was examined by a Yankees doctor and was not scheduled to go for an MRI or any other tests.

After the rain delay, Anthony Volpe led off the third with a single to right for the Yankees’ first hit. Trent Grisham walked and DJ LeMahieu’s forceout put runners on first and third with one out.

Inexplicably, however, when first baseman Romy Gonzalez fielded Rice’s grounder, stepped on first and fired to shortstop Rafaela, Volpe did not hustle all the way home. He turned to watch the play develop at second and had not yet touched the plate when Rafaela tagged out LeMahieu, preventing the run from scoring. That proved costly.

“I think he got crossed between foul ball and just didn’t know what happened,” Boone said. “But yeah, we’ve got to finish the play there and give ourselves a chance.”

Boone said he talked to Volpe during the game about the blunder. “He understands,” Boone said.

“I’ve just got to hustle all the way through there,” said Volpe, who said he thought it was a foul ball — which  doesn't really explain anything at all.

LeMahieu, who tried to sidestep the tag, also failed to get into a rundown, which could have allowed even a tardy Volpe to score if he had crossed the plate before LeMahieu was tagged out. The force was removed once Gonzalez stepped on first, as every Little Leaguer knows (and, apparently, not every major-leaguer knows).

Boone said of LeMahieu: “[Getting into a] rundown is the ideal thing in that spot.”

The Yankees, who had allowed the opponent to score first in 13 of the previous 14 games, scored first this time. They didn’t hit the ball out of the infield in the fourth and managed only one hit — the infield single on which Torres was injured — but scored three runs.

With the bases loaded, a throwing error on a potential inning-ending double-play ball handed the Yankees their first run. Volpe walked to make it 2-0 and end Tanner Houck’s evening. Grisham’s groundout gave the Yankees a 3-0 lead.

Gonzalez homered in the top of the fifth to make it 3-1.

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