The loss was the second in three games for the Phils, who have still won seven of 10. But it was the fourth consecutive loss in 2007 to Atlanta, and the third in the last at-bat variety, with two coming in extra innings in the Braves' season-opening sweep at Citizens Bank Park, prior to Monday night's walk-off.
The three runs Alfonseca (1-1) yielded were the first allowed by the Phillies bullpen in 15 1/3 innings at Turner Field.
Alfonseca, who had been unscored upon in eight appearances prior to Sunday afternoon, had relieved Brett Myers, who pitched a rocky, albeit scoreless, eighth. But the 19 pitches Myers threw were too many for him to come back out.
"I thought about [bringing Myers back out] but he's been out there three out of four, he threw 43 pitches the other night," explained Manuel. "He had kind of a strenuous eighth inning and this is a new role for him. I felt like it was time to take him out of the game. Alfonseca's been real good against left-handed hitters, and I figured it was a good time to put him in the game and we'd keep [Tom] Gordon back to close the game."
Lefties had been hitting .118 against Alfonseca, but the strategy backfired, as lefty leadoff hitter Kelly Johnson singled, then, after a fielder's choice on a bunt erased Johnson, Alfonseca walked lefty Chipper Jones, setting up the game-winning blast by Andruw Jones, his fifth of the season.
Mike Gonzalez (1-0) pitched a scoreless ninth to get the win for Atlanta, which has won three of four.
Philadelphia managed only four singles on the night, three of them in a two-run sixth inning of Atlanta starter Tim Hudson and none after Howard's two-out RBI single that gave Philadelphia a short-lived 2-1 lead. Hudson frustrated the Phils getting 19 groundball outs.
"Hudson was tough," said Manuel. "He threw up a lot of ground balls. He struck out one but he kept the ball down. He had it going good enough that we were chasing balls down out of the strike zone."
"Hudson had his stuff today," agreed Howard. "He was sinking the ball, moving it in, had good movement on every pitch. He was on his game tonight. You have to tip your hat."
Chipper Jones' eighth homer of the season leading off the sixth tied the game at 2 right after the Phils' two-run uprising.
Phillies starter Jon Lieber allowed two runs and seven hits over seven innings, throwing 109 pitches, 64 for strikes, but he admittedly labored.
"I felt fine but I know I could have pitched a little bit better," said Lieber, who struck out two but walked a career-high six batters. "I felt like I wasn't as sharp as I'd like to have been. But the guys really picked me up and played great defense behind me."
His best pitch was the double-play ball, inducing three, including a key twin-killing from Andruw Jones with two on and one out in the seventh to keep the game tied. Lieber also retired Hudson with the bases loaded and two out in the sixth.
"He got some huge double plays," said Manuel. "The double plays are probably what kept him in the game."
Hudson went eight innings for Atlanta, allowing two runs and four hits. He struck out one and walked one in throwing 94 pitches, 64 for strikes. The Braves righty faced the minimum through four innings and didn't allow a hit until Aaron Rowand's line-drive single in the fifth. Rowand left the game after the sixth with a back problem and is day-to-day.
The Phillies bunched the other three hits together in the sixth, when they overcame a 1-0 deficit. Jimmy Rollins, who finished the month at .297, reaching base in 20 of 24 games, singled and Shane Victorino singled to put runners at the corners. Chase Utley scored Rollins with a sacrifice fly that chased Andruw Jones to the warning track, then Howard laced a two-out single to give Philly a 2-1 lead.
The Phillies would not get another baserunner the rest of the night, as Hudson retired the last seven batters he faced and Gonzalez had a 1-2-3 ninth.
"It's tough to lose today but it kind of sums up how April was for us," said Howard. "April's done, so now we go into May, turn over a new leaf and get back after it tomorrow."