"We just haven't been hitting," a frustrated Manuel said. "On a bad night, we should score 3-4 runs."
This is an Astros staff that entered the game with a 4.24 ERA.
Adding insult was the fact that Houston's winning pitcher was former Phillie J.A. Happ, who was traded last month to the Astros as part of the deal for pitcher/leftfielder Roy Oswalt.
Happ allowed two runs in 61/3 innings. He threw 104 pitches, struck out four, and walked two.
"It was good," Happ said. "I'm relieved it's over."
He admitted this wasn't a normal outing.
"There were definitely some nerves going out there," Happ said. "I didn't know how I was going to feel. Like usual, once you get out there and get going, it was just another game."
Halladay is now 16-9, and in his nine losses the Phillies have scored a total of 20 runs.
With the Phillies trailing 3-2 with two outs in the ninth inning, Ryan Howard delivered a pinch-hit single to left field against Brandon Lyon. Domonic Brown, pinch-hitting for Ben Francisco, ended the game by striking out.
"This one is a tough one to swallow and we just have to go out [Thursday] and get them," Howard said.
Halladay retired the first 11 batters before Pence hit a 2-0 fastball for a solo home run in the fourth inning.
Happ had a no-hitter until Jayson Werth led off the fifth inning with a line-drive home run to left field.
Bourn made it 2-1 with a one-out home run to right field in the sixth inning.
Other than Happ, Bourn may have been the most unlikely player in the Astros' lineup to take Halladay deep. While Pence and Werth have combined for 37 home runs this season, this was Bourn's second home run of the season and 11th of his career.
Both home runs were hit on Halladay cutters.
"The one to Pence was middle up and the one to Bourn we were trying to go up and in and kind of left it in his hot spot down and in," Halladay said. "Not great pitches."
This wouldn't have been a game in this wacky series without another umpire moment. In the sixth inning, Phillies centerfielder Shane Victorino started toward first after being hit by a pitch in the left arm on a 0-2 count.
Not so fast, said home plate umpire Brian Knight, who ruled that Victorino didn't attempt to get out of the way of a 78 m.p.h. curveball.
The loud and unhappy reaction by the 106th consecutive sellout crowd was predictable: Boo!
Victorino made it a moot point with a base hit to left field, putting runners on first and second with one out.
Placido Polanco then tied the score with an RBI double over the head of leftfielder Carlos Lee that scored Halladay who had opened the sixth with a single up the middle.
Houston regained the lead in the seventh on Quintero's RBI single.
Trailing 3-2, Halladay, who threw only 73 pitches, was taken out of the game for a pinch-hitter in the seventh inning. Raul Ibanez, batting for him with runners on first and second and one out in the seventh inning, flew out.
"You want to keep pitching and I definitely understand first and foremost you are trying to win the game, not build up innings," Halladay said. "I definitely feel it was the right thing to do, but as a pitcher you always want to keep going."
The frustration continued for the Phillies when Ben Francisco was picked off third base to end the seventh inning.
"It was a bad play and has been addressed," Manuel said.
That was Quintero's sixth pickoff this season, which leads the major leagues. Manuel said he agreed with the umpire's call.
He then continued to express confidence in his team, as if there is any other alternative.
"I know if we play to our potential we can find our way out of it," Manuel said. "It's just a matter of us getting going."
Contact staff writer Marc Narducci at 856-779-3225 or firstname.lastname@example.org.