Hunter Pence's walk-off double off Bob Howry with none out in the ninth was the deciding blow, but a Cubs offense that managed just four hits and none after the fifth inning shared in this defeat.
"It was a good pitched game, we got a solo home run and that was it; it's hard to win with one run," Cubs manager Lou Piniella said. "We scored two [in the game] prior to the break, we scored one today. I don't know if it's a combination of too much rest or too little. Whatever it was, we lost, 2-1. Houston played a good ballgame. [We'll] come out here tomorrow and do the best we can, that's all."
The four hits were only one more than the Cubs' season low. The top five in the order -- Ryan Theriot, Kosuke Fukudome, Derrek Lee, Aramis Ramirez and Geovany Soto -- were a combined 2-for-19 with zero RBIs. The good news is that the Cubs might be without leadoff man Alfonso Soriano for just five more games.
"It's obvious that we've been straining, and we've got some people in the lineup not swinging the bats, to boot," Piniella said. "It makes it a little more difficult, so let's just ride this out as far as we can and get [Soriano] back in the lineup and see where we go from there."
Pence's double off Howry (3-3) into right-center scored Miguel Tejada with the winning run as the Cubs dropped the opener of the three-game series.
"The one to Tejada was at his shoulders," Howry said. "I was trying to get him to chase it, but he still got to it. The one to Pence was in, but he got his hands in and it was probably mid-thigh."
Lilly bounced back nicely from his last start, a 2 2/3-inning loss to Cincinnati, his shortest outing of the season. The left-hander exited after seven innings and held the Astros to a run on six hits. He struck out six and walked two.
"Lilly pitched good, battled," Piniella said. "[He] gave us seven good innings of baseball, pitched well enough to win. So did their guy."
Lilly's shutout bid came to a halt in the seventh when he tried to slip an 89-mph fastball by Carlos Lee. Lee turned on the inside pitch and sent it into the left-field seats for his 22nd homer of the season and a tie game.
Lilly wanted the pitch to be a little more inside and slightly lower.
"But I kind of got underneath the ball a little bit and cut it, so it was a little bit flatter," Lilly said. "The good thing was, as far as he hit it, it still only counted for one [run]. I've gotta believe that's about as good as you can hit it. He's going to do that when you leave balls out [over the plate]."
The Astros went on to load the bases with two outs in the seventh, but the left-hander avoided further damage by getting a ground out off the bat of Houston second baseman Kazuo Matsui.
"You had the feeling it was going to be a game where you really had to limit your mistakes, and I think for the most part we did that, but unfortuately I made one late to a good hitter," Lilly said. "I'm happy with the way that I threw the ball, but I couldn't be happy with the result. The whole point of going out there is winning, regardless of what it looks like. I think that you've got to give them a little bit of credit, especially Brian [Moehler], he pitched very well tonight. It didn't look like to me that he left too many pitches out over the plate."
The Cubs had gone ahead, 1-0, when Jim Edmonds, leading off the fifth, belted a 2-2 pitch from Moehler an estimated 357 feet to left for his 11th home run of the season.
A Mike Fontenot double one out later followed by a two-out walk to Theriot would be the final Cubs baserunners of the evening. The last 13 Cubs batters went down in order.
"Just a well-pitched, well-played game, a lot of first-pitch strikes," Theriot said. "You try to see some pitches and you end up getting into a hole. You can't really read into it too much. Just one of those games. The good news is we've got one tomorrow, too."
Jim Molony is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.