Finn Mikko Ilonen, the overnight leader, followed his opening course-record 64 with a 68 to stay in front on 10-under 132.
Ilonen was two shots ahead of Frenchman Romain Wattel (65), England's Robert Rock (66) and Northern Irishman Graeme McDowell (66).
McIlroy, who was joint 23rd at the U.S. Open on Sunday, had been looking to move to the top of the Race to Dubai money list and back into the top five of the world rankings.
"It's very frustrating," said the Northern Irishman, who won the BMW PGA Championship at Wentworth last month.
"To make six birdies and an eagle and shoot just two under means there were a lot of mistakes and wasteful shots.
"To miss the cut for the second year in a row is not a nice position to be in. I don't know what else to say, it's very disappointing."
McIlroy needed to finish birdie-eagle to qualify for the weekend and although he holed from long range on the 17th and hit a brilliant escape from the trees on the last, he was unable to chip in from the front of the green.
"I'm proud of myself how I fought out there," added McIlroy after his first missed cut on the European Tour in 2014. "I just need to tighten it all up and become a lot more consistent, make the bad shots a little bit better and not be as wasteful around the greens."
(Reporting by Tony Goodson, editing by Tony Jimenez)
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