Wood (1-2), pitching with two extra days of rest, gave up four runs -- one earned -- on seven hits and two walks in his shortest start of the season. The right-hander, coming back from arthroscopic surgery on his right shoulder, had gone at least five innings in his three previous starts.
"It's a long process," Wood said. "We're in the middle of it now. I sure would like to get to the end of the tunnel and see the light. I can't reach it yet. It's more difficult mentally than it is physically to get out there and not have good stuff every time you go out there. You have to learn to pitch."
Wood came into the game needing one strikeout for No. 1,300 of his career. He did not strike out anyone.
"He threw the ball pretty good," Cubs manager Dusty Baker said. "He tried to make a super play on that bunt which led to that three-run inning. He was trying to stop them from getting any, and ended up getting some by going to third instead of taking the out."
Preston Wilson doubled to lead off the Astros second, and one out later, Eric Bruntlett walked. Rodriguez then bunted, and Wood fielded the ball and threw to third but his throw skipped past Aramis Ramirez for an error, allowing Wilson to score.
One out later, Burke tripled just past right fielder Jacque Jones' outstretched glove, driving in two runs to put the Astros ahead, 3-0.
"It's usually never good when you go 3 2/3 [innings]," Wood said. "Most of the time, it doesn't work out well for you. The bunt play cost us a run. Jacque made a great effort on that ball in the gap. That's the way it went. It would've been easier to get out of that if I didn't throw it away."
"It was going to be a spectacular play if he made the play," Cubs second baseman Todd Walker said of Wood's play. "He made an excellent chance at it, and it didn't work out. If you give away runs, it's going to be tough to beat this team."
What should Wood have done?
"In hindsight, take the out [and throw to first]," Baker said. "If he makes a good throw, Wilson is out and it would've been a great play. He just didn't execute the throw properly."
The Cubs have won their last two series, and still have a chance to take this one with a win on Wednesday.
Wandy Rodriguez (7-3) picked up the win, as the Cubs dropped to 5-12 against left-handed starters.
The Cubs were batting .316 in their last 11 games, but Rodriguez stymied them, as he scattered five hits over seven innings and struck out one.
"He had us taking that first fastball early in the count and had us biting on bad changeups," Baker said of the Astros lefty. "He threw a ton of changeups. He was effectively wild. We have to find a way to get on these lefties."
Walker doesn't think the problem is the direction the ball is coming from.
"The record would indicate that but I don't think there's any correlation," Walker said. "It's not that you throw a lefty and we're going to lose. It's too early to tell."
Berkman belted his 16th homer with two out in the Astros fourth. Morgan Ensberg then doubled off Wood, who was pulled. He'd thrown 75 pitches, but Baker said they decided that was enough.
"The slider wasn't real sharp," Wood said. "It was more of a 'get me over' slider than a real two-strike, out-pitch. I tried to work with it and throw more changeups and move the ball around, but I caught too much of the plate."
Wood is hoping he'll be able to go on regular, five days rest and start on Sunday. The Cubs are hoping he keeps making progress.
"He's not quite there," Baker said of Wood. "He's on the way. He's just not quite there."