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PITTSBURGH -- The Pirates plan to build around pitching, defense and more pitching in the years to come, and the mid-market model was in display at PNC Park on Friday night.

At 55-39, the San Diego Padres entered the game in first place even though they ranked 14th in batting average, 12th in runs and 12th in home runs among National League teams.

At the same time, they also were first in fewest runs allowed, first in fewest hits allowed and third in fewest walks allowed in the league.

The Padres followed the formula in the opener of the weekend series, as they made a little bit go a long way in a 5-3 victory.

Their main offensive weapons: the sacrifice fly and base on balls. They had three of one and seven of the other.

"They're patient hitters that really don't try to do too much," said Pirates starter Paul Maholm, who took the loss.

"In the innings they scored, we walked too many people," manager John Russell said. "You just can't give them free passes. We walked some guys and (the game) got away from us."

The Padres even got a free pass from home plate umpire Bill Welke in the first inning. Welke ruled that Jose Tabata did not touch the plate while he attempted to score on a groundball, but replays clearly indicated that the rookie brushed his left hand over it.

In a game in which few runs were scored, the decision could have been crucial to the outcome.

"Definitely, I was kind of surprised when (Welke) didn't call anything at the beginning because I know for sure that my hand touched the plate," Tabata said through in interpreter afterward. "I was kind of surprised that he saw that play the way he did, but he told me that he didn't see me touch the plate, which is why he didn't make the call (immediately)."

"I think (Welke) knew that he probably had look at it on replay to be right," Russell said. "He said that he didn't see the hand go in there. It did. It's just one of those calls that we didn't get. (The run) could have helped, obviously."

Starter Kevin Correia (7-6) and three relievers limited the Pirates to six hits, only one for extra bases.

"When you have a 3.00 earned run average as a team, that means you'll win a lot of games," Russell said. "They're phenomenal at clutch hits. When a runner is on second base, they get a big hit, but their (success) is predicated toward pitching. They know that they'll be in every game. They pretty much know that they'll shut an opponent down. There's a lot of confidence in that for their team, I would imagine."

In his last five starts, Maholm (6-8) followed an effective performance with an ineffective one, and the trend continued to large extent in this one. He allowed four runs on nine hits and two walks in six innings.

A misread in the field didn't help Maholm in the second inning, when the Padres broke out to a 4-0 advantage.

"In the second inning, I really can't say that they hit a ball hard," he said. "They found holes, a broken-bat double . . . It was the kind of inning that happens, but I felt good. I still felt that I could throw pitches where I wanted to and keep us in the game."

Aaron Cunningham hit a line drive that Tabata allowed to sail over his head for a triple that opened the floodgates. The next two batters reached base, after which Correia singled home the first run.

"I don't want to make excuses, but I knew (how) a right-handed hitter hits the ball that way," Tabata said. "The ball took a different spin. I thought that I was in control, but I finally realized that the ball was over my head."

Jerry Hairston Jr. (sacrifice fly), Chris Denorfia (double) and Adrian Gonzalez (sacrifice fly) accounted for the final three runs.

"(Maholm) threw the ball well it you take away the second inning," Russell said. "Unfortunately, that was the inning that beat him. You can't spot a team like that four runs early. They pitch very well, obviously."

In the fourth inning, the Pirates sliced the deficit in half, as Lastings delivered a two-run single. Jason Jaramillo bounced into a double play to kill the threat.

One inning later, a Tabata groundout made it a 4-3 game, but Correia and the bullpen shut the door thereafter.

The Padres added an insurance run off reliever Brendan Donnelly without the benefit of a hit in the seventh inning.

Donnelly walked the first three batters, and the 18,611 fans on hand were none too thrilled about it. After reliever D.J. Carrasco entered the game, third baseman Pedro Alvarez made a nifty play to throw Denorfia out at the plate, but pinch-hitter Will Venable followed with a fly ball that scored a run.

Donnelly said that he didn't feel right on the mound for some reason, but the problem was not related to a health issue.

"If I do well, the fans cheer, and if I stink, they boo," he said. "I get it. The way that I pitched tonight, I would have booed, too."