Two of those birdies came after he was forced off the course due to a 1 hour, 43 minute rain delay.
The 24-year-old Bowood ace eventually carded a 75 to finish three over par and just a shot behind McIlroy, with American Kevin Kisner setting the clubhouse target on eight under par.
With three wins including two WGC titles, Matsuyama's season has undoubtedly been a success.
It took Phil Mickelson 31 holes to make his first birdie of the tournament, sinking a putt for a two on the 184-yard fourth, his 13th hole of the day. "Other than that, I would have been just fine".More news: Chardan Raises Price Target on Editas Medicine
"Didn't do anything great today but I didn't do anything bad".
On Saturday, the elements appeared to have affected a player who had seemed unflappable for much of the last two weeks.
The Queenslander, 2015 US PGA Championship victor and runner-up a year ago, bogeyed the 11th immediately after play resumed.
Coming off his second World Golf Championships victory last week after shooting a record-tying final-day 61 at the Bridgestone Invitational, Matsuyama credited his improved putting for Friday's score.
A thunderstorm that halted play for almost an hour and 45 minutes came after Matsuyama had made three consecutive birdies starting at the 12th hole, but he took advantage of wet conditions when play resumed and added birdies at the par-5 15th and par-3 17th.More news: HBO offered $250K to hackers to buy time, leaked email says
"I'm happy I'm in the position I'm in", Kisner said. "So, to actually get away with a five, I actually felt pretty good about myself going to the next tee". Then again, only one player in the top 15 through three rounds at the 99th PGA Championship has any major hardware to his name - Louis Oosthuizen, who is T-4 and 2 shots back. He made four bogeys in five holes on the front side, then answered with birdies at the par-5 seventh and par-4 eighth. 15 and 17 to get back to even par for the day. 14-16, only to be stuck with a double-bogey on the final hole. So not only did the Austrian fail to move the cut line, he wound up missing the cut with that bogey on his last hole.
McGirt will stay in the Tar Heel state for next week's Wyndham Championship in Greensboro at Sedgefield Country Club.
After starting day three of the year's final major just two shots off the pace, the Australian world No.7 crashed out of contention spectacularly with a six-over-par 77 at Quail Hollow in North Carolina.
That dropped Kisner from 10-under, following birdies in his previous two holes, to eight-under and a temporary tie with Chris Stroud.More news: Backlash swift after Democratic congresswoman calls the NRA a security threat
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