Reliever Joel Hanrahan (0-2), who had not allowed a hit in two innings of relief, walked Houston's Kazuo Matsui to open the bottom of the ninth with the game tied. Matsui stole second base, advanced to third on a wild pitch by Jesus Colome and scored on Carlos Lee's single to center.
"You can't win ballgames by walking people, and that's what I did," said Hanrahan, who walked five in 3 1/3 innings, though two were intentional.
"I'm just not throwing strikes. Maybe I'm trying too hard and it's getting in my head. When I throw the ball over the plate, I have good results."
Matsui was the only Astros player to walk and score, but Washington manager Manny Acta knew the walks did more damage than that.
"When you walk the bottom part of the order, you pay for it, because you roll the lineup over," he said.
Hanrahan walked pinch-hitter Jose Cruz Jr., who is hitting .091, with two outs and nobody on in the eighth. So instead of only having to face the top three in the Houston order in the ninth, if he had retired them 1-2-3, Hanrahan had to walk red-hot Lance Berkman intentionally.
That brought up Carlos Lee, whose two-run double in the eighth beat the Nationals, 6-5, on Tuesday night.
Acta brought in Colome to pitch to Lee. It didn't help. Lee lined a ball to center that Lastings Milledge might have caught, but Matsui could have tagged and scored easily.
"It made no sense [to catch the ball]," Acta said of Milledge. "[Matsui] was going to score anyway."
Starter Odalis Perez, still trying for his first win of the season, gave the Nationals everything he had.
Perez pitched five innings and allowed three runs, including a home run to Berkman. He hit Ty Wigginton later in the same inning and gave up a two-run single to pitcher Roy Oswalt.
"He was sick," Acta said of Perez. "He was puking after the first inning. It was a great effort. He paid for it, giving up the two-run single to Oswalt."
Left-hander Mike O'Connor, who will move into the rotation when he starts on Saturday night vs. Florida, pitched a scoreless seventh in relief with the game tied at 3.
"He had to pitch," Acta said of getting O'Connor ready for Saturday night. "He hadn't pitched in a while. We couldn't get him in the game [Tuesday]."
Hanrahan showed how good he can be, striking out Lee and getting Hunter Pence to fly out to center with one out and runners on first and third in the seventh.
Matsui walked to lead off the seventh, stole second and moved to third on Miguel Tejeda's grounder to the right side.
"It's a situation I probably shouldn't have been in in the first place," Hanrahan said.
"We like his stuff," Acta said of Hanrahan. "He struck out Lee and worked his way out of that [seventh] inning. It's about his consistency."
Three of the Astros stolen bases led to runs, including the winner.
"They're just running," Acta said of the Astros. "We need to do a better job of holding the runners. You don't run on the catcher."
"They had a couple of stolen bases off me," Hanrahan said. "I tried varying my time. They got some good jumps off me."
"They were being aggressive and getting really good jumps," catcher Paul Lo Duca said. "I can't really answer [why]. I made a pretty good throw to second on one."
But the runner was still safe.
The Nationals scored all their runs on a pair of homers by Ryan Zimmerman, his fourth and fifth. He hit both off Oswalt, a two-run shot in the first and a solo in the sixth.
"I'm starting to have better at-bats and hitting the ball hard," said Zimmerman, who is 5-for-9 in the series. "The loss is tough. We played two good games here and came out short on both of them. If we come out [Thursday] and salvage one and go home, we'll be fine."
Lo Duca reinjured his right hand swinging at an Oswalt pitch in the seventh inning. Lo Duca, who returned from the disabled list just last Friday, had been hit by a pitch on the hand April 13. He said he will undergo an MRI on Thursday.
Three Astros fans sitting in the first row behind the Washington dugout were ejected from the game soon after Lo Duca departed.
"A couple of guys were obnoxious since the game started and we alerted security," Acta said. "They were flat out [swearing] from the beginning. It started from the first at-bat."
Lo Duca said one of the fans challenged his manhood as he was coming off the field.
"I said come meet me after the game," Lo Duca said. "He turned redder than a ketchup bottle."