He struck out David Ross, which Halladay and catcher Carlos Ruiz thought was the third out of the inning, but home-plate umpire Gary Cederstrom ruled Ruiz did not catch the ball. As Halladay and Ruiz walked off the field, Ross went to first to keep the inning alive.
The right-hander, who was facing a bases-loaded jam after giving up two runs, escaped the threat by getting Paul Janish to pop out to Ryan Howard in foul territory.
Halladay, who spent seven weeks on the disabled list earlier this season, is the fourth active pitcher with 2,000 or more strikeouts, joining Andy Pettitte, CC Sabathia and Kevin Millwood.
"We made some changes mechanically," said Halladay. "It's going to take some getting used to, but pitch-wise, I thought there was better movement. The cutter was better. The curveball was better. It was a good step, but I need to keep working on it and be more consistent with it. I definitely felt like it was a step in the right direction; things were better."
There are just 67 pitchers in baseball history with 2,000 or more strikeouts.
Halladay, who surrendered six hits, three runs, one walk, two home runs and struck out seven over six innings in his sixth loss, didn't talk about the milestone, instead focusing on the Phillies' struggle this season.
"There have been a lot of damaging moments," he said about this season. "It's getting frustrating. We have no choice but to keep playing. Regardless of what we did coming into this and what we have in front of us, I think we owe it to the fans, ourselves and the organization to go out and turn things around."
Todd Zolecki is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.