McIlroy's hopes of successfully defending his title effectively disappeared with a triple-bogey seven on the fifth, but the former world number one battled back to record a closing 70 at Oak Hill.
The 24-year-old has still posted just one top-three finish this season compared to five wins around the world in 2012, but was pleased with his performance after making four birdies in six holes towards the end of his second round to simply make the cut.
"I played the best golf of the week today [Sunday]," said McIlroy, who finished three under par, seven behind champion Jason Dufner. "I hit some really good drives and really good iron shots. Didn't quite putt as well as I did the first three days, but really, really happy with my game going into the next few weeks.
"It's a very big step in the right direction. I saw a lot of great signs out there today [Sunday]. Hopefully I can just bring that through to the next few weeks and have a strong finish to the season.
"I made a big number on five (although) I hit a good shot, exactly what I wanted to do with it. It just pitched in the exact wrong place. Everything else feels pretty good."
McIlroy finished one shot ahead of fellow Northern Irishman Graeme McDowell, who closed with a 66, and Scotland's Marc Warren, who recovered from an opening 74 with rounds of 67, 68 and 69.
That gave the 32-year-old from Glasgow a share of 12th - easily his best finish in a major - and he said: "I'm very delighted. I didn't play great on Thursday but to finish in a major, especially the PGA, with three rounds in the 60s is very pleasing.
"I felt really comfortable and confident over everything I was doing. The last few days felt very stress-free which is unusual on a golf course as tough as this.
"It's just another kind of step in the right direction I suppose, a decent finish in the majors which is something I had not done before, so it's nice to tick it off.
"I've played the Open, the US Open and the PGA, so the Masters is the only one missing for the 'Warren Slam'."
David Lynn, runner-up to McIlroy last year, finished as the highest-placed Englishman again in a tie for 22nd on level par, with Lee Westwood and Paul Casey on three over.
Westwood had been tied with McIlroy on three under but struggled to a closing 76 and has now played 63 majors without a victory.