The U.S PGA champion four-putted the 10th green, his last of the tournament, to cap a frustrating two-over-par 72 round which gave him a total of five-over 145, 14 shots behind leader Michael Campbell.
"I had a great start getting it to four under and in a position from which I might have even won the tournament but then it all went on the slide," Northern Irishman McIlroy said.
"Now I am going to work on few things with my putter before playing in Dubai next week," added the 23-year-old who missed the cut for the first time since the U.S. Open in June.
McIlroy knew he had to shoot low in the second round after opening with a three-over-par 73 at the Hong Kong Golf Club on Thursday and, starting from the 11th tee, he did just that producing four early birdies to get under par and within four shots of the lead.
However, at the par-five third hole, his 11th of the day, he put his approach shot into a greenside bunker and after missing out on a good birdie opportunity, his charge up the leaderboard came to a halt.
A putt to save par at the fourth hole lipped out, at the seventh he misjudged the speed of the green and three putted and another shot was dropped on the following green when he put his first putt six feet past the hole and failed to hole the return.
"The wheels came off at that par five, it was a huge momentum breaker," said McIlroy, who sealed the European Tour's money list last week with a third-place finish in Singapore.
The cut was set at two over par.
New Zealander Campbell, who has endured a seven-year slump since winning the U.S Open in 2005, holds a one-shot lead over the field after seven birdies in a second-round 64 that took him to nine under for the tournament.
On hearing McIlroy would not be playing the last two rounds, Campbell declared with a smile: "That makes winning the UBS Hong Kong Open a lot easier."
China's Zhang Lan-wei, Miguel Angel Jimenez of Spain and Swede Fredrick Andersson Hed are tied second on eight-under 132.