McIlroy produced a battling finish to avoid a fourth missed cut in five appearances in the event, although scraping through on the mark of level par left the 25-year-old 12 shots behind halfway leader and Ryder Cup team-mate Martin Kaymer, who added a 69 to his course record-equalling 63 in the opening round.
It also meant an early start for McIlroy yesterday and he again struggled on the front nine, making a bogey on the first, double bogey on the fourth and a bogey on the sixth before birdies on the seventh and eighth took him to the turn in 38.
As on Friday, the back nine came to the former world No 1's rescue and birdies on the 10th, 11th, 16th, 17th and 18th ensured a round of 69 and three-under-par total. So far this week, McIlroy has taken 117 strokes on the front nine and 96 on the back nine, a difference of 21 shots at an average of seven per day.
McIlroy was finished hours before the leaders were due out, Kaymer holding a one-shot lead over American Jordan Spieth, who is the only player in the field not to record a bogey in the first 36 holes. "If I had just kept it around even par for the front nine, I'd be up near the leaders," McIlroy said.
"I'm happy with how I've been able to come back the last couple of days, but it's also a little frustrating because I feel I'm playing good enough to not have these little stretches of bad holes.
"Maybe tomorrow I can put it all together and start strongly and finish strongly like I have the last few days."
World No 2 Adam Scott had also made the cut on level par after a second round of 67 and matched McIlroy's 69 to join the Northern Irishman on three under.
That kept alive Scott's hopes of overtaking Tiger Woods at the top of the world rankings with a top-16 finish, although Henrik Stenson can also claim top spot with a top-six finish and the Swede had eagled the second to move joint 10th on five under.
o Scotland's Scott Henry holds the clubhouse lead going into today's curtailed Madeira Islands Open. Organisers decided after yesterday's play was again suspended due to bad weather that a cut to the top 65 players and ties would take place after the first round is completed today, with the tournament now scheduled to finish tomorrow.
o Scotland's Vikki Laing is one shot behind Czech teenager Klara Spilkova for the final round of the Turkish Airlines Ladies Open at National Golf Club in Antalya. A bogey on the ninth, her final hole, cost Laing a share of the lead after she started with three birdies and an eagle in her first five holes, the 33-year-old from Musselburgh eventually signing for a four-under-par 69.
"I'm happy with it," Laing said. "I made a bunch of birdies at the beginning. I hit the ball well and made a few good putts. I'm just trying to hit fairways and greens so I'll have the same plan for tomorrow."
After Friday's play was washed out, Spilkova, 18, added a 70 to her opening 69 to lie seven under par in pursuit of her first Ladies European Tour title. Denmark's Malene Jorgensen is two shots off the lead on five under, with England's Charley Hull three under alongside first-round leader Heather MacRae, who could only add a 76 to her opening 67.