Despite a Wrigley Field throng of 39,889 chanting his name, Wood declined to take a curtain call after his seventh-inning strikeout of Jeff Kent, whose two-run double in the fifth turned out to be the decisive blow.
Houston right-hander Wade Miller outpitched Wood, holding the Cubs to one run on five hits in six innings to push them 3 1/2 games back in the National League Central Division.
Wood became the fastest pitcher to reach the 1,000-strikeout plateau, doing it in 134 games and 853 innings. The previous record-holders were Roger Clemens, who reached the 1,000-strikeout mark in 143 games, and Hideo Nomo, who accomplished it in 9272/3 innings.
"That's an awesome milestone," Cubs manager Dusty Baker said. "Especially since he's so young in his career and the fact he missed a year. He came back from a serious arm injury, came back throwing the ball great. It's something for him to be proud of. I'm sure he would've traded that for a victory."
Wood (11-9) also has a league-leading 201 strikeouts, the fourth time he has reached that mark. But the Cubs' offense was silent again. They're hitting .163 over the last four games with six runs scored.
Kent, who came in with a .526 career average against Wood, snapped a scoreless game in the fifth with a two-run double over the head of center fielder Doug Glanville. Eric Karros' bloop RBI single off Miller in the sixth made it 2-1, but Miller (9-10) promptly struck out Damian Miller and retired Augie Ojeda on a pop to short. Baker said he would have pinch-hit for Ojeda, but his bench was short due to Kenny Lofton's wrist injury.
The Cubs got a break in the eighth when right fielder Richard Hidalgo dropped Aramis Ramirez's popup, but Ramirez was thrown out at first after turning the corner for second and failing to get back in time. Ramirez said he had to be aggressive, "especially when they have [Octavio] Dotel and those guys in the eighth and ninth."
Craig Biggio slammed a Kyle Farnsworth pitch off the flag pole in left to make it 3-1 in the ninth, and Billy Wagner notched his 34th save with a scoreless ninth.
"Nobody hands pennants over," Wood said. "We have to go out and earn it."
The Cubs have been resilient all season, shaking off untimely injuries, the controversies over Sammy Sosa's corked bat and Baker's remarks about black players' tolerance for heat, and, of course, the recent invasion of the gnats.
Now their backs are against the wall again.
"Maybe it was already written or meant to be," Baker said. "We didn't want the corked-bat incident, and when I said what I said [about race] I didn't think it was going to be a major thing like it was. That's how life is sometimes. Sometimes adversity makes you closer.
"Sometimes you've got to have faith that everything will work out. You're either going to roll over and die and quit, or keep fighting and fighting."