Lurking in a large cluster of players who shot 68s is Brooks Koepka, who has won four majors in the past two years - two U.S. Opens and two PGA Championships - and finished second at the Masters and U.S. Open this year.
Shane Lowry nearly chipped in for an eagle on the short par-four fifth, the tap-in birdie taking him into a tie for the lead with Holmes.
Meanwhile New Zealand's Ryan Fox blew out with a four over par 75 to slip from a share of third to a tie for 59th, nine shots off the pace.
The home favourite posted the joint best round of the day with a six-under 65 to get back to two-over, but missed out by just one shot with the cut at one-over.
But it was the performance of Lowry that had the crowd in raptures, the Irishman birdieing four of the first five holes.
"I just want some time off just to get away from it", Woods told reporters.
"God it was just unbelievable".
"And I think the reason I'm so good mentally now is I know". It was a day that I'll remember. I'm in a great position.
With Molinari surrendering his hold on the Claret Jug he would love nothing more than close friend Tommy Fleetwood, with whom he struck up such a devastating partnership at last year's Ryder Cup, to break his major drought.
From there Lowry was able to make par and he took full advantage with birdies on the 15th and 16th, the latter courtesy of a stunning tee shot to seven feet on a 232-yard par-three which fully deserves its name "Calamity" due to the danger lurking to the right of the green.
"Oakmont was so long ago and I was a lot younger". "But it's nice to get two rounds in a row".
Woods has openly admitted he is having to adapt his schedule in order to prolong retirement having struggled with injuries in recent years, which culminated in four back surgeries.
A brilliant bunker save on the 15th, a smart up-and-down after being short and right on the vast "Calamity Corner" par-three 16th prefaced a highly-eventful par on the 17th where, distracted by TV commentary from the tented village maybe 80 yards behind the tee-box, he leaked his drive into the customers on the right.
McIlroy will miss out on the weekend along with Tiger Woods, who shot a one-under 70 but still ended six-over for his two rounds. "I was probably as nervous as I've been in quite a while on the 1st tee, nearly ever, I'd say". He gave a somewhat-depressing interview in the aftermath, telling reporters he just wants to "go home" after the past few weeks.
"I'm obviously going to be thinking about it tonight".
Inevitably he was reminded of how, three years ago, he blew a four-stroke lead at the U.S. Open, at Oakmont, finishing with a six-over 76 to finish tied for second, three strokes behind victor Dustin Johnson. A bogey at the seventh halted his momentum but he birdied 10 and 11 to get the fans roaring.