The former world No.1 posted a sparkling nine-under-par opening 63 at Emirates Golf Club - the scene of his first European Tour title win in 2009 - but struggled to a more pedestrian second round of 70.
That put the Northern Irishman on an 11-under-par total of 133, giving him a one-shot halfway lead over the American Brooks Koepka, whose flawless 65 equalled the lowest score of the day. England's Danny Willett also shot 65 to share third place on eight under alongside Ireland's Damien McGrane and France's Julien Quesne, with the defending champion, Scotland's Stephen Gallacher, and Henrik Stenson among seven players another shot back after a 67.
Tiger Woods, the world No.1, playing alongside McIlroy, could only manage a 73 to make the cut with just a shot to spare on three under.
McIlroy revealed he had felt ill during his round but refused to use that as an excuse. He said: "It wasn't too bad, there were a few stomach cramps. We got some takeaway food last night [Thursday] that obviously did not agree with me.
"This morning I was not feeling too good before coming to the course but I don't think it affected the way I played. It was a little uncomfortable but it did not stop me from hitting some good shots out there and I am definitely not going to make any excuse for not playing my best today.
"I will just go back tonight and regroup and realise I am still leading the tournament. I hit a couple of loose drives which I haven't done the last couple of weeks but I still feel like I'm playing well enough to go and win the tournament."
Koepka earned "battlefield promotion" to the European Tour last season by winning three times on the Challenge Tour, his last victory coming at the Scottish Hydro Challenge in Aviemore before a quick dash to Sunningdale the next day to qualify for the Open Championship.
"I've never played with Rory, so it's going to be fun," said the 23-year-old who lives in Florida. "I know him a little bit from seeing him around, so hopefully I'll be able to play as well as I did today."
Gallacher remains the leading Scot after shooting 71 to sit on seven under par, one ahead of another past Dubai winner, Colin Montgomerie (70). Paul Lawrie (71) is on five under.
Chris Doak revealed after shooting four-under 68 that he is taking painkillers for a knee injury after slipping on the wet driveway of his Glasgow home when moving his golf gear from one car to another five days before heading to the Middle East for what is also his honeymoon.
"It was wet and part of the pavement is painted; I just slipped," he said. "I had my bag on my shoulder and a ball and tees in my hand and I fell heavily on my left knee.
"The physio guys here in Dubai have looked at it and they've diagnosed a bruised bone but I'm not conscious of it when I'm swinging, and it's only sore in the morning. Besides, painkillers do the job."
Five birdies helped Doak move to five under par and make it six of seven cuts in the 2013/14 wraparound season. "I didn't really played that well today, so I'm very happy," he said. "I was a wee bit indifferent off the tees but managed to calm down and score well, while my putting was pretty good with just 29 putts."
David Drysdale was left ruing a two-stroke penalty he called on himself three holes from the finish that led to a missed cut. Drysdale, who has battled his way through the pain of a bulging disc, was five under playing the 16th hole when he stepped forward to brush loose grass off the line of his putt.
He realised he had also come into contact with a spike mark and immediately called a penalty on himself. John Paramor, the chief referee, confirmed the two-shot penalty. The result was a triple bogey and a 73.
Derek McKenzie, the Elgin-born director of golf at the Santiburi Samui GC in Thailand, was disqualified from his first European Tour event after rounds of 77 and 81. The 41-year-old is friendly with another Thai-based Scot, Simon Yates, and had been afforded a personal invitation to compete by Mohamed Juma Buamaim, vice-chairman and chief executive of Golf in Dubai.