Paulino had three RBI and tagged out Vinny Castilla for the final out as Pittsburgh beat the Padres 6-4 on Saturday night.
"Everybody has been swinging the bats well," Paulino said. "Everyone is playing together. We are getting better as a team. We stayed aggressive."
The Pirates have won seven of their last nine, but needed a heads-up play in the ninth to secure the victory.
With runners on first and second and one out with a run already in via a Josh Barfield sacrifice fly, Dave Roberts grounded to shortstop Jack Wilson, who flipped the ball to second baseman Jose Castillo for one out. Castillo's throw to first was low and got past first baseman Sean Casey.
Castilla rounded third and headed for home, but the ball bounced perfectly off the railing back to Casey, who alertly threw home to Paulino to retire Castilla.
"The ball caromed and I went to get it," Casey said. "I didn't think he was running, so it caught me off-guard. I just tried to get it to (Paulino) as fast as I could. And he made a great play."
Thanks in part to that play, Gonzalez was credited with his seventh save in as many chances.
"Your first instinct is go," Castilla said. "I'm half way, and the ball bounces back to (Casey). But at that point, you have to keep going."
Castilla would not have represented the tying run for the Padres, who had a three-game winning streak snapped.
"On a bad throw, you think you can make it, so you go," Bochy said. "But in that situation, it is not worth the risk."
The peculiar ninth inning overshadowed what had been a solid start by Zach Duke (4-6), who had lost his previous four starts before earning the win Monday over the Milwaukee Brewers. He allowed San Diego three first-inning runs, but settled down after that and permitted only one hit over the next six innings. He struck out four and walked three.
"I was impressed with the way that we responded to San Diego's three-run first inning," Pittsburgh manager Jim Tracy said.
The Padres took their lead on Khalil Greene's three-run double after a rain delay of 1 hour, 36 minutes. But the Pirates answered back with five runs in the bottom half of the inning.
"Any time you get five runs in the first, that's something you just say, 'My team's behind me; now I owe it to my team to go out there and keep us on top,"' Duke said.
Greene's two-out double scored Mike Cameron, Brian Giles and Mark Bellhorn, giving the Padres a 3-0 lead before the Pirates came to bat for the second straight night.
Pittsburgh scored all five of its runs in the first with two outs.
A Jeromy Burnitz single scored Jack Wilson. Two batters later, Jose Castillo hit a ball that caromed off of both third baseman Vinny Castilla's and shortstop Greene's gloves that was ruled a single. Jason Bay scored on the play.
"It was just one of those games," Padres starter Mike Thompson said. "It's not like they were hammering home runs."
Paulino then singled to right to drive in Burnitz and Freddy Sanchez, and Duke helped his own cause when Castillo scored on his single up the middle.
Rookie Mike Thompson (2-2) endured the worst start of his young career. The 25-year-old had won two of his first three starts -- not allowing more than three earned runs in any of them. But he was tagged for six runs (five earned) on eight hits with no strikeouts.
"He pitched a lot better than the numbers indicate," Bochy said. "It's a tough night for a kid. I thought he threw the ball all right."
The Pirates, who are 14 games under .500 for the season, improved to 16-5 in night games played at PNC Park. ... Castillo has reached safely in 19 of his last 22 games. ... The Pirates have a 53-inning errorless streak. ... The Padres have lost six of their last eight home games after starting the season 12-4 away from PETCO Park. ... Padres reliever Brian Sikorski made his first major-league appearance in six years.