Marquis (6-5) gave up six runs, eight hits, and three walks over 4 2/3 innings, striking out three. He now has one win in his last 11 starts.
"He wasn't too sharp," said Cubs manager Lou Piniella. "He was up with the ball today. He didn't have real good sink. Usually when he has good sink, he gets a lot of ground balls. He wasn't doing that today."
"I wasn't making pitches when I needed to," Marquis said. "I felt I was getting ahead of hitters pretty decent tonight, and I was giving them too many good pitches to hit in the middle of the plate. I didn't make the adjustment like I wanted to and put my team in a hole."
The right-hander had a strange first half. Included in his wins was a three-hit shutout against the Pirates on May 9. Then, he struggled to notch any wins.
"My numbers are my numbers," Marquis said. "Physically and mentally, I feel great where I'm at. It's just a little hiccup in today's game. Break time, get a little rest, and get back to work in a week or so."
The adjustments are minor, he said.
"Very minor," Marquis said. "I know what I felt out there, so I have an idea of what I want to do in my bullpen session and into my next start. I'll keep working on it until I get better."
Maholm (5-11) improved to 4-0 against the Cubs in his career, holding them to five hits, two walks and striking out five over seven-plus innings.
"He's locating all of his pitches, No. 1," Cubs infielder Ryan Theriot said of Maholm. "We were watching video, and he's throwing three different pitches first-pitch for strikes, as he did today. He didn't really pattern at all, and when you have a guy locating all of his pitches, especially his breaking ball, it keeps you off balance. You almost have to look for one pitch and hope he makes a mistake, and he didn't make a mistake today."
Nady, who was 3-for-4, including an RBI double in the sixth, and Ryan Doumit each singled to start the Pirates second. Two outs later, Jack Wilson walked to load the bases for Maholm, who then singled to center to make it 2-0.
"I don't know if [Marquis] pitched around the eighth hitter or not," Piniella said of the approach with Wilson that inning. "The pitcher was hitting .160. For a hitter, that would probably equate to .300."
That's baseball math. Bottom line, Maholm came into the game batting .138 with two RBIs and he doubled that.
"That was a big hit for them," Piniella said. "Bases loaded, two outs, the pitcher gets a two-out hit and gets a couple runs in. We come back and tie the ballgame, and before you know it, they hit two out of the ballpark. We didn't pitch well tonight, and that was really the story."
The Cubs did answer in the third. Rob Bowen ended an 0-for-22 skid when he doubled to lead off, and was safe on Marquis' sacrifice despite Maholm's throw to third. Marquis also was safe, and advanced on Alfonso Soriano's sacrifice fly to center, making a head-first slide into second. One out later, Maholm's first pitch to Derrek Lee skipped in the dirt and Marquis scored on a wild pitch to tie the game at 2.
Sanchez put the Pirates on top with a leadoff homer in the third, launching an 0-1 pitch into the first row in left. One batter and three pitches later, Nady hit his 14th homer to go ahead, 4-2.
The Cubs haven't connected much lately, and rank 11th in the National League in homers.
"We've been winning baseball games," Piniella said. "I don't really concern myself too much with home runs."
The Cubs needed one in the eighth. They had two on and nobody out when Maholm was pulled. Shawn Chacon walked Lee to load the bases, and Aramis Ramirez and Mark DeRosa each hit sacrifice flies for the final runs.
The problem was pitching. Piniella tried to forget about it quickly, and was thumbing through a boat magazine after the game. Marquis will be watching video.
"I just didn't make pitches when I needed to and left a lot of balls in the middle," Marquis said. "They're professional hitters and they capitalize on the mistakes."