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.
Halladay tied a career high with 14 strikeouts and tossed his seventh complete game.
Bryan Shaw (1-0) tossed a scoreless eighth and J.J. Putz worked the ninth for his 30th save. Putz fanned Jimmy Rollins with the tying run on second.
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.
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 singled, Victorino lined his 13th homer into the right-field seats for a 2-1 lead.
That was seemingly all Halladay needed. He was on top of his game in the eighth, fanning Kelly Johnson, Willie Bloomquist, and Ryan Roberts on curveballs in the mid-70s.
His only miscue was his first balk of the season in the fourth.
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: 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 late broadcaster, Harry Kalas. Kalas died in 2009.