"We needed one more out from Lilly," Piniella said. "I had Carlos Marmol ready to come in to pitch, and we didn't get it. Lilly pitched a good ballgame. One more out and we bring Marmol in to face [Lastings] Milledge, but we didn't get to that."
The loss extended the Cubs' losing skid to three games and dropped their record against the Pirates to 1-7 this season.
"They play very well against us," Cubs outfielder Alfonso Soriano said. "We lost the game tonight, and we got to try to come back and win tomorrow. I don't believe in bad luck. We're not playing good right now, and they are playing well against us."
Lilly, who tossed seven shutout innings in his last start against the Dodgers, allowed three runs on six hits in 7 2/3 innings. He took the loss and fell to 1-5 on the season.
"Second place, it's not that good here," Lilly said. "It's giving up fewer runs and winning the game, that's what it's about as a team. Obviously it's pretty evident that I've got to do my job."
The Pirates got six strong innings from right-hander Jeff Karstens, who limited the Cubs to two runs on six hits. He received a no-decision. The Pirates got good work from their bullpen, with Javier Lopez and Joel Hanrahan hurling scoreless frames in the seventh and eighth innings. Hanrahan notched the win, improving his record to 2-1.
Octavio Dotel pitched a scoreless ninth inning to record his 12th save for Pittsburgh.
Piniella made several lineup changes Tuesday to spark the Cubs' slumbering offense, one of which paid dividends in the top of the third inning. After a Kosuke Fukudome triple, Xavier Nady -- playing first base in place of the struggling Derrek Lee -- smacked a two-run home run, giving the Cubs a 2-0 lead. It was the third home run of the season for Nady.
Nady made a strong bid for more playing time, going 4-for-4 with a home run, a double and two RBIs. Nady is still recovering from elbow surgery and trying to get healthy.
"Yeah, it's been good," Nady said. "Each day it seems to get a little better. I'll just keep working on the rehab, and hopefully in the long run it's a nonissue down the stretch."
Pittsburgh looked as if it had nicked Lilly for a run in the bottom of the third inning, when Karstens singled and appeared to have come around to score on a double by Milledge, who was thrown out trying to stretch a double into a triple. But the umpires ruled that Milledge was out at third before the run scored, so the lead remained 2-0 Cubs.
The Pirates cut the Cubs' lead to 2-1 in the bottom of the fourth inning, when Garrett Jones clubbed his seventh home run of the season into the right-field seats. It was Jones' 12th RBI against the Cubs this season.
"I don't know. Being from Chicago, I guess, maybe pumps me up a little bit," Jones said of his numbers against the Cubs. "I grew up a [White] Sox fan, so maybe there's something down deep there."
Frustration is starting to set in with the Cubs, who had hoped to turn things around on this road swing.
"I'm not going to talk about it anymore," Piniella said. "We got beat, and we'll go out and get 'em tomorrow, and do the best we can. That's all we can do."
"It's frustrating on everyone," Nady said. "Obviously you come prepared, and you plan on getting big hits and getting things going, but offensively we're just not doing it, and there is no way around it. Lilly pitched a heck of a game, and we're just not swinging the bats well and not driving in runs and having big innings. It's just carrying over."
George Von Benko is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.