Lilly (12-9) entered the game with a Major League-leading 1.60 ERA at home and a 1.53 mark in his past seven outings. But he had not pitched in 12 days because of tendinitis in his left shoulder, and manager Lou Piniella said he looked "a little rusty."
Lilly had four walks in his past four games but walked two of the first three hitters and gave up a single to Milledge. With the bases loaded and one out, Steve Pearce hit a potential double-play grounder to second, but Milledge barreled into second and upended shortstop Ryan Theriot, who was unable to get off a throw. That kept the inning alive and permitted Pittsburgh's first run to score.
Although second baseman Andres Blanco shouted at Milledge after the play, it appeared that Milledge avoided incurring an interference call by keeping his hand on the bag as he slid into Theriot.
"It was a clean slide, it was just a lot of contact," Milledge said. "We're both out of the playoffs, so they probably felt like we shouldn't play [hard], but it's just the nature of the game. We're going to continue to play hard. A lot of guys on this team are playing for spots on the team next year. We can't slack off. We have to continue to play hard. We have to continue to improve."
Theriot was not upset after the game.
"I never felt it was a dirty play," Theriot said. "He hit me with his shin, and he could have hit me with his cleats. That's how you play the game. I'd do the same thing, and almost as players, we're expected to do that. He's playing hard, and you take guys out, and that's what you do."
Milledge's slide became crucial when Jason Jaramillo came up next and smacked a two-run double. Brian Bixler followed with an RBI single to put the Pirates ahead 4-0.
That was plenty of support for Morton (5-9), who gave up 10 runs and recorded three outs in his last start at Wrigley Field, on Aug. 14. This time, Morton had little trouble with a lineup that was missing Derrek Lee and Aramis Ramirez, who were held out with minor ailments. Morton gave up four hits and didn't allow his first knock to the outfield until the sixth.
"Charlie Morton threw the ball really well," Lilly said. "He was pumping a lot of strikes, changing speeds and throwing his breaking ball for strikes. He did all the things today you're taught to do coming up in the Minor Leagues."
Lilly rebounded from his rough first to shut down the Pirates over the next six frames and finish his 2009 campaign with a career-best 3.10 ERA. He said he was happy with the way he threw strikes and worked the outside corner this season, but that did not make the year a success in his mind.
"I'm not real satisfied with it," said Lilly, who made seven fewer starts than in 2008. "The first thing is there wasn't an opportunity for myself or any of us to get the chance to pitch in the postseason. And then I missed time, so I'm not happy about that. One of the goals I have going into the year is be a guy the club can rely on to make all the starts and rack up innings, and I wasn't able to do that."
Piniella was more complimentary.
"I thought during the course of the season, [Lilly] was our pitcher," he said.