Zambrano won his seventh straight decision since rejoining Chicago's rotation, combining with two relievers on a four-hitter, and the Cubs held on to beat San Diego 1-0 on Monday night to knock the Padres out of the NL wild-card lead.
The Padres, who loaded the bases with two outs in the ninth before pinch-hitter Nick Hundley flied out to left, dropped one-half game behind the Atlanta Braves, who beat the Florida Marlins 2-1 in 11 innings.
"Nobody likes to lose, whether it's April or September," Padres manager Bud Black said.
The Padres fell a game behind idle San Francisco in the NL West race. After three more games against the Cubs, the Padres end the season with three weekend games in San Francisco.
Zambrano (10-6) outdueled Tim Stauffer, holding San Diego to three hits over seven innings. He struck out five to pass Charlie Root for second place in club history with 1,436. He walked four.
Zambrano said his mother saw him pitch for the first time.
"I knew she was there," said Zambrano, who is from Venezuela. "She kind of inspired me. Today was a special day."
The big right-hander is 7-0 with a 1.27 ERA in 10 starts since returning to the rotation on Aug. 9. Following a June 25 dugout blowup, Zambrano was banished to the restricted list. He underwent anger management therapy, then made three relief appearances before getting his starting job back.
"Thank God that he blessed me with this end of the season. I read the other day in the paper, 'the former ace.' If you can count, you can see if I'm the former ace or if I'm still the ace of this team along with the other guys. I have confidence in myself," Zambrano said.
"This is a little bit different Carlos than we've seen in the past," San Diego's David Eckstein said. "The Carlos that we've faced before had that hard, 95 mph sinker. Tonight it wasn't as hard, but he was cutting the ball and especially was elevating that fastball just a little bit at the top of the strike zone, which was hard to get on top of. He was mixing in his split-finger and keeping guys off-balance. He's doing a great job."
Carlos Marmol pitched an eventful ninth for his 35th save in 40 chances. He struck out the first two batters before Yorvit Torrealba reached on an infield single, sliding headfirst into the bag. Everth Cabrera pinch-ran for Torrealba and stole second before Marmol hit Chase Headley on the right foot. Tony Gwynn Jr. walked to load the bases before Hundley flied out.
"This club just doesn't give up," Eckstein said. "We always try to find a way to put ourselves in a position to come up with that hit. We've done it a lot. It just didn't happen tonight."
Stauffer (5-5) held the Cubs to three hits through six innings before Chicago broke through. Alfonso Soriano doubled to left and scored on Blake DeWitt's single to center. DeWitt and Marlon Byrd each had three hits.
The Padres threatened in the seventh, Zambrano's final inning. Matt Stairs drew a leadoff walk and Headley walked with one out. But Zambrano got Gwynn to fly out to center and pinch-hitter Oscar Salazar to foul out.
"He's just attacking the zone with confidence," Cubs interim manager Mike Quade said. "He should be successful when he does that. One more good start in Houston and that will be some kind of finish. He's been fantastic."
Stauffer tied his career-high by going seven innings, allowing one run and five hits. He struck out five and walked two.
The Padres had runners on first and second and two outs in the first when Nady fielded Stairs' hard grounder and stepped on the bag to end the threat. Nady made another big play in the second. After Torrealba drew a leadoff walk, Nady leaped to catch Headley's line drive and doubled off Torrealba.
With runners on first and second in the top of the fifth, Eckstein made a diving stop of Kosuke Fukudome's grounder and flipped it to Tejada to force Zambrano at second for the third out.
In the sixth, Starlin Castro's grounder glanced off Stauffer and Tejada barehanded it and threw him out.
"When you come here, this is what you expect -- good pitching, good defense, on the edge of your seat for nine innings," Quade said. "They live it every day. When you come in here as a visitor, it's really something."
Padres ace Mat Latos will try to bounce back from a three-game losing streak Tuesday night when he's scheduled to start opposite Ryan Dempster. ... Padres LF Will Venable was a late scratch with a bad lower back, an injury that sidelined him earlier in the season. Stairs started in his place. ... Stauffer is 2-2 with a 1.91 ERA in his last six starts.