SAN DIEGO — The Pittsburgh Pirates have seen enough of the San Diego Padres.

Andrew Werner allowed two runs over six-plus innings in his major league debut and Carlos Quentin drove in three runs, leading the Padres to a 4-2 victory over the Pirates on Wednesday.

The win not only completed San Diego’s three-game sweep but gave the Padres their 18th win in 21 games against Pittsburgh.

“This team has presented us nothing but trouble,” Pirates manager Clint Hurdle said. “I wish I could make something of it other than you want to stop it. I don’t know the reason why. We don’t take them lightly. They’ve been a pretty bit formidable for us.”

San Diego also put a crimp in the Pirates’ playoff plans as they dropped 8 1-2 games behind first-place Cincinnati in the NL Central.

While Pittsburgh remains in the wild-card hunt, its play will have to improve.

The Pirates have lost 15 of 24 since July 28, when they were two games behind Cincinnati in the division and led the NL wild card.

NL batting leader Andrew McCutchen said he needs to step it up if the Bucs are to stay in contention.

McCutchen went 1 for 5 as his batting average dropped to .349. McCutchen, who has only two home runs and 11 RBIs since July 18, went 3 for 15 in the series.

“I’m not happy with how I’m swinging the bat right now,” he said. “I’m a lot better than where I am right now. I’ve still got to keep working hard. I know it’ll change.”

Werner could barely believe he was facing McCutchen.

“If you have told me two years ago, I would be facing Andrew McCutchen in a big league game, I would have told you that you were crazy,” Werner said.

But he struck out McCutchen to end the first inning and handled the rest of the Pirates with ease.

“He was hitting his spots, which makes most pitchers effective,” McCutchen said. “He kept the ball down. He could get hurt if he leaves stuff up, but he didn’t do that.”

Quentin had three RBIs for the second straight game, including a two-run double in the first inning and an RBI single in the fifth.

Werner, a 25-year-old who was called up from Triple-A Tucson earlier in the day, allowed four hits, walked four and struck out two.

Brad Brach, Luke Gregerson and rookie Tommy Layne finished the four-hitter. Layne pitched the ninth for his first major league save.

Werner was coming off one of his worst starts of the season in which he allowed a season-high eight runs in 4 1-3 innings.

But he kept Pittsburgh off balance and had allowed only Pedro Alvarez’s fourth-inning RBI single heading into the seventh. After Gaby Sanchez led off the seventh with his fourth homer and Werner walked Alvarez, the rookie was lifted.

San Diego gave Werner a big lift by scoring three runs in the first inning off James McDonald (11-6) on only one hit.

“I was out of rhythm. You can’t walk guys,” McDonald said. “This is a team that sees a lot of pitches. They know the strike zone well . . . I got a better feel as the game went on.”

McDonald gave up four runs and five hits over five innings. McDonald walked five and struck out two.

The Pirates, who have lost four of five, were swept in a three-game series for the first time since losing at Baltimore in June.

McDonald started the first inning by issuing consecutive walks to Everth Cabrera, Will Venable and Chase Headley.

Quentin came a few feet away from hitting a grand slam when his fly ball hit off the wall in left-center field for a two-run double.

Mark Kotsay followed with a sacrifice fly.

McCutchen reached on a one-out single in the fourth. After a walk, McCutchen scored on a Pedro Sanchez’s two-out single.

Cabrera stole two bases to raise his season total to 24 without being caught. Cabrera set a club record with his 28th consecutive stolen base, dating to Sept. 10, 2010.

Notes: McCutchen finished the season series against San Diego hitting just .184 (5 for 27) with no homers and two RBIs. . Since 2006, the Pirates are 6-16 at Petco Park. ... Werner was San Diego’s 14th starting pitcher this season, one shy of the club record set twice. ... Jerry Mumphrey held the previous Padres record with 27 straight stolen bases in 1980... . With their 7-5 loss in 10 innings on Tuesday night, the Pirates were the last team in the majors to lose an extra-inning game. ... Pittsburgh is off Thursday before hosting Milwaukee on Friday. ... San Diego has Thursday off before it travels to Arizona on Friday.