Meanwhile, Brandon Backe battled through 6 2/3 innings, giving up three runs in the first and solo home runs in the third and fifth frames.
"He was up in the zone today," said Astros manager Cecil Cooper of Backe. "He didn't really have that crispness to his fastball, and he didn't have the command."
Russell Martin scored off a double by James Loney that bounced on the left-field foul line before going into the stands in the top of the first, and Blake DeWitt followed with a two-run single to score Loney and Jeff Kent. Andre Ethier had a solo home run on the first pitch of the third, and Loney had another solo shot three innings later.
"I felt like I made a decent pitch to Loney, he just blooped one in there," Backe said of the first-inning double. "It's one of those things that's been going on with me all year, just little hits like that. If that ball goes foul in the first inning and I get the out, there's no telling what happens."
Backe (5-9, 5.22 ERA) gave up just one hit in the other innings, and Cooper said the right-hander found his breaking ball and his offspeed pitches in the third and fourth innings.
But Backe said he saw no positives from the outing, despite striking out eight batters.
"I get absolutely nothing," he said. "I get a loss. I'm tired of losing, just like I'm sure everybody else on this team is. We want to get back to where we were in the month of May, when we were playing well. Games like this don't help very much."
The Astros did manage a small rally in the fifth, as Geoff Blum reached on a fielding error by second baseman Angel Berroa. A single by Hunter Pence sent him to second, and J.R. Towles' double to left scored the two. Backe walked before Michael Bourn grounded out to end the inning.
"Everybody battled out there," Towles said. "Sometimes you have good days, and sometimes you don't, and when you don't, you have to battle. [Billingsley] had good stuff. Any time you can go eight innings with two runs and none earned, that's a pretty good day."
Towles had another big chance in the ninth with men on second and third, but flew out to the shortstop to end the game. He said that despite the loss, he felt good about getting the only two RBIs of the day for Houston.
Billingsley's pitching had the entire Astros team baffled. Lance Berkman and Bourn went hitless.
"Today, that's the best I've seen these guys pitch," Houston outfielder Carlos Lee said. "All his pitches were on the corners, and he didn't really give us anything to hit."
As if the day was not rough enough, reliever Doug Brocail was ejected by home-plate umpire Tim Timmons after walking Matt Kemp in the top of the ninth. Brocail had yelled an expletive at himself and pounded his glove after throwing ball four, but Timmons thought the curse was meant for him.
"I guess I'm supposed to be quiet and keep my mouth shut and not care that I'm trying to win a ballgame, too," Brocail said. "We're trying to win a ballgame and trying not to put anybody on base, and I give a free pass."
Brocail said he was frustrated that batters can argue calls with the umpire when they strike out, but a pitcher cannot show emotion.
"I told the umpire, 'Hey, it's not you. It's him. He's disappointed he didn't throw the ball in the strike zone,'" Cooper said. "And [Timmons] just said he couldn't display the type of action that he displayed on the field."
The mistake has happened before. In a previous outing, Brocail was allowed to stay in the game when catcher Humberto Quintero explained to the umpire that Brocail was upset with himself and not the call.
The Astros are just three series away from the All-Star break, and after winning the two series before they faced the Dodgers, Cooper said he has learned a few things about the team.
"The guys continued to battle and play hard," Cooper said. "We didn't get the same type of starting pitching the last three games that we'd gotten in the last eight or 10, but we still had a chance to win those games. That's key."
The Astros were disappointed with the series loss after winning Game 1.
"We just didn't play particularly well the last three games," Berkman said. "A lot of that has to do with the fact that they have one of the most underrated pitching staffs in the game.
"We didn't do a whole lot offensively. It seems like whenever we put together a good streak, we're swinging the bats well, and we didn't do that in the last part of the series."
Krysten Oliphant is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.