"You cannot let that run come in to home plate," Dotel said. "After I get those guys with two strikes, if they're going to score they're going to do it against my best which is why I came back with my fastball."
Paul Maholm, who pitched six effective innings for the win, had to turn away when the game got dicey in the ninth.
"I was in the dugout," he said. "I just had my head down. I just kind of listened to the crowd to get the feel for it. He likes to make things interesting, he's an interesting guy."
Ryan Church hit a two-run double and McCutchen added an RBI single for Pittsburgh, which has won the first two games of the series after being swept by Cincinnati at home.
McCutchen went 2 for 3 with a walk after going 5 for 5 with a homer in Friday's 10-6 victory. He is 11 for 14 against the Cubs this season.
Clement was in a 5-for-33 slump before connecting for his fourth homer.
"He's making progress," Pirates manager John Russell said. "He's still blocking a little bit but he's starting to get the bat head to the ball. Obviously against Marmol in the ninth, that was huge and gave us a little breathing room."
The Cubs have lost seven straight against the Pirates dating to last season, and nine of their last 11 overall. Ryan Dempster (2-4) pitched seven solid innings but lost his fourth consecutive start, allowing three runs and four hits with five walks.
"We had chances offensively, especially in the bottom half of the ninth, but, boy, that big hit is really elusive," Cubs manager Lou Piniella said.
Piniella had two good chances to at least tie the game. Theriot entered the day batting .320 and Byrd was at .345.
"Did I feel good about it? Yeah, I felt good about it, but I don't feel good about it now, but I felt good about it then," Piniella said. "What are we going to do? We've tried a little bit of everything."
Dempster struggled to find the strike zone in the first inning, issuing consecutive walks to Aki Iwamura and Andy LaRoche to open the game. McCutchen blooped a single to right to score Iwamura with his sixth consecutive hit. One out later, Church doubled down the right-field line to make it 3-0.
"When you walk the first two guys it makes the inning a whole lot tougher," Dempster said.
In their previous series against the Reds, the Pirates scored only one run while losing three straight.
Maholm (3-3) allowed two runs and eight hits. He struck out four and walked none.
Aramis Ramirez, who entered hitting .168, hit a two-out, two-run double in the third for the Cubs. Ramirez was waved home by third base coach Mike Quade when Geovany Soto followed with a single to left, but he was easily thrown out by Church.
"You have to take a chance when you aren't hitting, you got to take a chance and it didn't work out," Ramirez said.
Church was caught by surprise when the Cubs decided to test his arm.
"I don't know what they were doing," he said. "I'd take throwing out somebody over the hit. Right there, that ballgame is 3-2 so it was a big run. I saw it and was like 'OK thank you!' I love throwing."
Iwamura is hitless in his last 26 at-bats after going 0 for 2 with two walks.