The Australian recovered from a double bogey on the seventh to fire seven birdies in eight holes and finish the day in a tie for third just two shots behind leader Jimmy Walker.
First round leader Walker continues to lead the tournament after a 66 helped him reach nine under par, where he was later joined compatriot Robert Streb.
That was 12 better than Mcilroy, who was out of sorts from 100 yards and in and around the greens all day.
A 35-foot birdie putt on 17 backed up by a huge drive on 18 looked to set Mcilroy up to sneak inside the cut line, before a loose iron and a poor chip condemned him to a second missed major cut of the year.
The Northern Irishman’s next major will now be the Masters at Augusta next April.
Partner Phil Mickelson played the 18th perfectly to birdie and make the cut by one shot – despite driving out of bounds off the first and carding a triple bogey seven.
It was a good day for some of the pre-tournament favourites, with Open Champion Henrik Stenson shooting 67 to reach six-under, while 2010 PGA winner Martin Kaymer went round in 69 to sit one shot further back.
-9 Jimmy Walker, Robert Streb
-7 Emiliano Grillo (ARG), Jason Day (AUS)
-6 Henrik Stenson (SWE)
-5 Martin Kaymer (GER) Patrick Reed, Brookes Koepka
-4 Hideki Matsuyama (JPN), Jamie Donaldson (WAL), Rickie Fowler, Harris English
Selected Others (GB Unless Stated)
-3 Jordan Spieth (USA)
-2 Paul Casey, Andy Sullivan
-1 Lee Westwood, Andrew Johnston, Tyrell Hatton, Ross Fisher
+1 Phil Mickelson (USA)
+1 Danny Willett
+3 (MC) Rory Mcilroy
+5 (MC) Sergio Garcia
+9 (MC) Dustin Johnson (USA)
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