The Holywood star missed a golden opportunity to pull away from the field when he bogeyed the second and seventh despite the fact that the wind that made scoring tough for the morning starters eased in the afternoon.
While he played his last 11 holes in one-under, by following a birdie at the 12th with brilliant par saves on the 16th, 17th and 18th for a one-over 71, he has work to do to end his near eight-year wait for a fifth major win but believes he can do it.
"It wasn't the easiest day for me. I certainly didn't play as well as I played yesterday, but I hung in there, and I battled well," said McIlroy, who was one of just three players still under par to shoot a round over par yesterday.
"I made some good up-and-downs when I needed to. I could have converted a few more chances that I gave myself on the back nine, maybe, but overall, it was a day it could have got away from me, and I could have shot 73 or 74 and really would've had a big hill to climb.”
At four-under par, he's tied for fifth with Mexico's Abraham Ancer and 25-year old Korn Ferry Tour graduate Davis Riley, five shots behind Will Zalatoris.
The former Wake Forest phenomenon, who has yet to win a PGA Tour event but already has four top-10s in six major starts, carded a bogey-free seven-under 65 to lead by one stroke on nine-under-par from another ball-striking machine in Chile's Mito Pereira (27), who shot 64.
With the temperature set to plummet over the weekend and the wind forecast to switch direction, the 79 players who made the cut on four-over — including Tiger Woods, who is three-over after a gusty 69 —face a very different Southern Hills today.
McIlroy hinted he doesn't expect Zalatoris or his nearest challenger Pereira to keep it going under major pressure.
“The two guys are at the top of the leaderboard are very new to this position,” McIlroy said. "They've obviously played very well, but I thought the three up-and-downs on the last three holes were important just to keep myself within a few shots.
"It's still a great position to be in going into the weekend. There's a lot of golf to play and we're going to see a completely different golf course than we've seen the last couple of days.
"The wind is going to come from a completely opposite direction, so it's going to be a different test for everyone, and everyone's going to have to adapt to that."
McIlroy might not see Zalatoris or Pareira as the men to beat but rather Justin Thomas, who shot two 67s from the tough side of the draw to sit alone in third on six-under.
Another major champion, two-time Masters champion Bubba Watson, is solo fourth after making nine birdies in a brilliant 63 to trail Zalatoris by four shots on five-under.
Seamus Power is the next best of the Irish, tied for 23rd on level par after a 69, which is his first sub-70 round in a major.
Like Shane Lowry, who is 11 shots off the pace on two-over after a 72, both men will need rounds in the sixties to have a chance tomorrow.
Pádraig Harrington does not believe it's a course for chasers given the rough and the well-defended greens.
"It's an easier golf course to play patient golf on," said the Dubliner, who holed just one putt outside six feet all week as he followed his opening 77 with a 75 to miss the four-over cut by eight shots.
"If you're hitting it to 15-20 feet on every green and are rolling putts for birdie, you're going to hole a few.
"But if you're going after those pins, you're going to miss a few and if you miss and find those bunkers, you're struggling to get up and down."
Harrington returns to seniors golf next week for the second senior major of the season, the KitchenAid Senior PGA Championship at Harbor Shores Resort in Michigan.
But he does not believe his game is in poor shape, despite the result in Tulsa.
"Nothing went my way, that's it," he said. "I don't see anything in my game that I'm unhappy with. I putted well but never holed a putt. In the first round, I think I holed a four-footer for a par and everything else was less than two feet. You've got a hole some putts.
"Maybe it wasn't the best start ever. Taking six on the second hole yesterday didn't help. I certainly wouldn't read anything into the week in itself.
"You're going to get weeks like that, and hopefully, I get better weeks. Nothing went for me. That was it. There's nothing to fix."
Lowry will play with South Korea's KH Lee at 4.20 pm (Irish time) today with Power drawn with Cameron Tringale at 5.50 pm.
McIlroy is out with Ancer in the third last group at 7.30 pm, just ahead of Thomas and Watson before leaders Pereira and Zalatoris tee off at 7.50 pm Irish time.