SAN FRANCISCO — Cubs closer Daniel Palencia wiped the sweat from his brow with his sleeve as he crossed the chalk and headed for the dugout.

Behind him, the Giants were mobbing Jung Hoo Lee, who had just lined a walk-off single to beat the Cubs 4-3 and complete the three-game sweep.

It marked the first time all season that the Cubs had been swept in a series of at least three games.

“That’s kind of fun with numbers,” manager Craig Counsell said. “We’re just trying to add up wins and stack up wins. We didn’t do that this week. Need to get back to that this weekend.”

It’s true, the season-long first didn’t illustrate anything concrete about the Cubs’ performance. But their ability to avoid sweeps had stood as an example of their resilience.

“Coming off a sweep and then getting swept, it’s a little bit frustrating,” left fielder Ian Happ said, alluding to the three games the Cubs won against the Angels to kick off the three-city road trip. “And for us, taking a lot of pride this year in not letting that happen — and even when we struggled a little bit, taking one from a series.”

They fell just short of salvaging the series in that way on Tuesday.

“At least the last two nights, we didn’t capitalize on our run scoring opportunities,” Counsell said.

Besides a pair of solo homers, from Dansby Swanson in the second inning and Michael Busch in the sixth, the Cubs’ only other run came during a first-inning rally that ended abruptly.

With one out, Kyle Tucker jump-started the offense with a double down the left-field line. Then Happ drove him in on a ground ball through the middle of the infield.

Pete Crow-Armstrong kept it rolling with a single past diving first baseman Rafael Devers to put runners on first and third. But the inning came to a grinding halt as Nico Hoerner, one of the top hitters in baseball with runners in scoring position, grounded into a double play.

Two innings later, Tucker again got on base with one out. But Happ was called out on strikes as Tucker was thrown out attempting to steal in another inning-ending double play.

Happ and home plate umpire David Rackley exchanged words before Counsell stepped out of the dugout to argue on his team’s behalf. Rackley tossed Counsell, marking the manager’s third ejection of the season.

“I thought he had gotten off to a rough start with balls and strikes,” Counsell said after the game. “Frankly, thought it continued — for both sides, actually.”

After looking at it, Happ said the changeup that nicked the outside of the zone for strike three was indeed a strike.

In the ninth inning, Tucker got on for a third time, this time drawing a walk with no outs and the score tied.

Happ struck out looking, Pete Crow-Armstrong lined into a sliding catch by Lee in center field, and Hoerner flew out to center.

Up to that point, the Giants had scored all three of their runs on a pair of Willy Adames homers off Cubs starting pitcher Shota Imanaga.

In the first inning, Adames launched a first-pitch fastball near the top of the strike zone over the fence. So, in the sixth, Imanaga went higher.

Adames still got to the fastball and sent it just out of Crow-Armstrongs’ reach as the center fielder leaped and stretched over the wall in left-center field.

“That pitch was more to set up the next pitch,” Imanaga said through Japanese interpreter Edwin Stanberry after limiting the Giants to three runs in seven innings. “And, reflecting on it, that should have been more of a ball.”

Bench coach Ryan Flaherty went to Palencia, who had recorded 20 saves in 22 opportunities since mid-May, in the highest leverage inning of the night. Three straight singles decided the game.