A birdie on the 15th helped McIlroy to the turn in 35 shots, but he then bogeyed the second, third, fifth and sixth holes to lie outside the projected cut mark, before birdies on the seventh and eighth saw him safely through to the weekend.
Here are the latest odds to win the final major of 2017.
"I nearly had three (eagles) in a row because I hit it to an inch the hole before", he said.
The career Grand Slam will have to wait at least another year, but Jordan Spieth says that's no reason to be disappointed. "I've still got a few big tournaments left, so it's a question of whether I play in all of them or take some time off to get 100 percent healthy".
Day won the 2015 US PGA Championship and finished a shot behind 2016 victor Jimmy Walker.
"I'm going to approach the first two (playoff) events trying to obviously win, but looking to kind of crescendo into East Lake and peak there and consider East Lake a major at this point, as far as our preparation goes", Spieth said.
McIlroy paused for the longest time. "That's the next big thing on my radar".
The four-time major victor has been far from his best over the a year ago as he struggled with the injury he picked up in the close season, and has admitted to rushing back before regaining full fitness. You don't want to be teeing off at 09:45 on the final rounds of a major on a Sunday.
"An injury like this, it's eight full weeks of rest before you start to rehab it and then you go again", he said. "I've got this next week off to assess what I need to go forward". I felt like we took as much time as we needed to at the start of the year.
McIlroy said the pain wasn't as bad as it was early in the year at the Players, when he said it really flared up on him. If I'm capable of playing, I feel like, 'Why shouldn't you?' But then at the same time, if you are not capable of playing at your best, why should you play? But it's there and I can play 18 holes, but once I get done, having to go through the whole routine of getting it ready to go again the next day, you shouldn't have to do that. "If it was injury-free, that wouldn't happen".
Both players carded six birdies but also gave two strokes back with a pair of bogies. "That aggravated it a little bit", McIlroy said.
"I just haven't it allowed it the time to fully heal".
Spieth won't have another chance at major No. 4 until heading down Magnolia Lane in April, but he still believes there's plenty to play for as the season reaches what he termed the "fourth quarter". "But if I want to challenge on a more consistent basis, I need to get 100 per cent healthy".