With the 18th green only illuminated by the light from a scoreboard in the evening gloom, McIlroy two-putted from 45 feet for birdie to finish on the projected cut mark of one under par.
The start of Friday's play had been delayed by 80 minutes in the morning due to fog, meaning the four-time major winner will have to wait until the second round is completed on Saturday to learn his fate.
McIlroy's playing partner Ludvig Aberg maintained his brilliant form by sharing the lead with fellow Swede Sebastian Soderberg on 10 under.
Soderberg made an eagle on the 18th to complete a superb 64 and set the clubhouse target, which was matched by rising star Aberg.
However, a dramatic day was overshadowed by two ugly incidents.
As four groups of players waited on the 18th tee late in the day, Thomas Bjorn exchanged words with a drunk spectator ahead on the closing hole.
Just hours earlier, Robert MacIntyre revealed he was heckled by a spectator who said he had bet against him.
MacIntyre was playing alongside Ryder Cup team-mates Justin Rose and Matt Fitzpatrick and carded a 69 to make the cut.
However, the fact that he outscored Rose (71) and Fitzpatrick (72) did not go down well with a vocal fan who seemingly had money on a different outcome.
"The crowds were unbelievable, even though I was getting a bit of stick there coming up 17," MacIntyre said.
"There's obviously gambling going on in the game of golf nowadays and some people ride a lot of money on it and, unfortunately, he lost today."
Asked if the fan had told him he had bet against him, MacIntyre said: "Aye, he did and he told me the amount he had riding on it.
"It's all about gambling nowadays and I said to Greg (Milne, his caddie) walking to the 18th tee 'Be switched on as this guy could throw anything at us here so keep an eye on him and do your job'."
McIlroy was unimpressed by the late-night drama, saying: "The fog obviously delayed things but I've never remembered having that many players on 17 and 18.
"It's not as if they teed us off in tighter slots or anything.
"It's hard for me trying to play the last well and make the cut, it's a bit of a mad dash and a scramble to get finished. I don't know what you could do about that apart from less players in the field."
