Lyle Overbay quickly found his place as Arizona's latest late-inning star.
Halladay (15-5) had retired 12 straight batters into the ninth. Halladay, trying to become the NL's first 16-game winner, allowed consecutive singles to open the inning. Overbay hit a one-out double to right that silenced the crowd and helped Arizona win the opener of this three-game series between NL division leaders.
Overbay knocked in all three runs as Arizona won its seventh straight game.
"It's a good situation," Overbay said. "I couldn't ask for anything better."
The 34-year-old Overbay was released last week by Pittsburgh after hitting .227 with eight homers and 37 RBIs in 103 games. He was drafted by Arizona in 1999 and played with the Diamondbacks from 2001-03.
"We gave him a quick version of, 'Here we go,'" Arizona manager Kirk Gibson said. "He'll fit right in for us."
Halladay tied a career high with 14 strikeouts and tossed his seventh complete game.
Bryan Shaw (1-0) pitched a scoreless eighth for his first career win and J.J. Putz worked the ninth for his 30th save. Putz fanned Jimmy Rollins with the tying run on second. Putz is 9 for 9 since returning from the disabled list.
Overbay, who had one pinch-hitting appearance for the Diamondbacks, led them to their 35th comeback win this season.
"These guys have composure when we're behind," Gibson said. "These guys are a quick strike team."
Shane Victorino hit a two-run homer off Arizona starter Josh Collmenter in the fifth. Halladay took over from there.
Halladay, who also struck out 14 batters April 24 at San Diego, had again dazzled in front of the usual sold out crowd at Citizens Bank Park. The Phillies, an MLB-best 78-42, lost for the first time in Halladay's last 11 home starts.
He struck out the side in the fifth and eighth against the NL West-leading Diamondbacks and had his 14th career double-digit strikeout game. Halladay even atoned for a rare balk with his leadoff double in the seventh, his first career extra-base hit. He was batting .075 (4 for 53) entering the game and was hitless his first two at-bats.
Halladay threw 123 pitches and had one intentional walk.
Phillies manager Charlie Manuel never considered yanking Halladay in the ninth.
"It's kind of his game, isn't it?" Manuel said. "He's my ace. If I was going to make a move, I'd do it to start the inning."
He never before had to hustle to second base on a swing of the bat. Halladay hit a high fly down the right-field line off the wall against Collmenter in the seventh for the double, but was left stranded at third.
With the Phillies trailing 1-0 in the fifth and after Rollins had singled, Victorino lined his 13th homer into the right-field seats for a 2-1 lead.
His first balk of the season in the fourth was his only miscue — until the ninth.
"It can be a little tougher to swallow sometimes in the ninth then if you get blown out in the third," Halladay said.
Collmenter struck out a career-high eight and walked one in 6 2-3 innings. Overbay staked him to a 1-0 lead with an RBI single in the second.
Halladay vs. Collmenter could be a playoff preview. While the Phillies have a commanding lead in the NL East, the Diamondbacks have defending World Series champion San Francisco chasing them down.
Notes: The Phillies placed 3B Placido Polanco (back) on the disabled list. ... Phillies All-Star LHP Cole Hamels will skip at least one turn in the rotation with shoulder inflammation. Phillies GM Ruben Amaro Jr., says an MRI showed inflammation near the rotator cuff. ... The Diamondbacks purchased the contract of LHP Wade Miley from Triple-A Reno and placed right-hander Jason Marquis on the 15-day disabled list. ... The Phillies send Cliff Lee (12-7, 2.83 ERA) to the mound against Arizona's Joe Saunders (8-9, 3.76 ERA) on Wednesday. ... The Phillies unveiled a statue for their treasured former broadcaster, Harry Kalas. Kalas died in 2009. ... The Phillies signed 2011 draft pick OF Larry Greene. Greene, 18, was selected in the compensation round (39th overall). They also agreed to terms with second-round selection Roman Quinn (66th overall). The Phillies signed 30 of their 50 draftees, including nine of their first 10 selections.