Geovany Soto also hit a two-run double, and Jeff Baker added a solo homer, but it wasn't enough as Chicago fell nine games behind the St. Louis Cardinals in the National League Central. The Cubs, tied for first on Aug. 6, have lost 13 of their past 18 games.
"We have to get going," Cubs general manager Jim Hendry said. "We're running out of time. We need a great homestand. We put ourselves in the spot we're in."
Zambrano (7-5), on the disabled list because of back spasms, smacked his fourth homer with one out in the third off starter Garrett Mock (3-5) to tie the game at 1.
"It doesn't matter when you lose," Zambrano said of his homer. "My job is to pitch. I didn't do my job today. Nothing else matters."
"Zambrano wasn't very sharp," Cubs manager Lou Piniella said. "Hopefully, he's much better the next time out."
With one out in the Nationals' fourth, Willingham hit his 20th homer off Zambrano, and after Ronnie Belliard singled, Dukes hit an RBI double. Second baseman Mike Fontenot caught the relay throw but spiked the ball on the infield dirt for an error. Dukes, who had reached third on the miscue, was out on a botched squeeze play. He made up for that in the fifth.
Ryan Zimmerman hit an RBI single in the Nationals' fifth, and they eventually loaded the bases. Zambrano then walked Willingham to force in a run and prompt Piniella to make a switch. Aaron Heilman struck out Belliard, but Dukes drove the first pitch into the left-field seats for his eighth home run and a 9-1 lead.
Willingham also connected off Tom Gorzelanny in the eighth, hitting a three-run shot.
"We hit the ball well," Riggleman said. "It was a combination of that and getting [hits] off the end of the bat that fell in for us. It created big innings, bases-loaded situations and scoring situations that we passed up all day [Monday]. Today we didn't pass them up."
The good news for the Cubs is that Zambrano had no problems with his back. What about his pitching?
"This is the big leagues," Zambrano said. "I left some pitches in the strike zone. I was behind in the count too much. In the big leagues, when you're behind in the count and you make a mistake, you pay for it."
It'll be tough to catch the Cardinals with games like Tuesday's. The Cubs had hoped coming home would give them a lift but failed to deliver clutch hits with men in scoring position, a problem that has nagged them all season. Hendry has been under fire, as well, from critics who feel he's failed to deliver, too.
"I don't really think too much about it, to be honest," Hendry said of the criticism. "We've done a lot of good things the past couple years. We're having a bad year -- it certainly didn't meet my expectations."
Zambrano heard the boo birds in the crowd of 37,297 as he walked off the field in the fifth. The right-hander can be animated and has let his emotions get the better of him in the past.
"Look, he's got a personality," Piniella said. "The only thing I concern myself with is that he pitches well."
He didn't do that against the Nationals.
"That teams swings the bat, they have some athleticism, and they've been playing well," Piniella said. "We've had a rough August -- what can I say?"
The Cubs now have fallen to 8-14 in August, a dramatic switch after an 18-9 July. Piniella says he'll stick with the veterans for the final 30-something games.
"It's time for veterans right now," Piniella said. "We'll see how they perform. I fully expect them to perform well."
Ever the optimist, he still feels the Cubs have a chance.
"It's amazing what a nice winning streak will do for you," Piniella said. "You can make up ground in a hurry. Unfortunately for us, we haven't had a good winning streak for a long time. That's what I cling to."