McIlroy picked-up a headache late in his round of a five-under-par 67 brought on by the heavily contaminated air of the Chinese financial capital.
However, there was some relief when McIlroy punched his way through the pollution to land a 144-yard, nine-iron second shot at the last to just four feet and end with a birdie to trail Donaldson by five shots.
“I started to get a bit of a headache on the back nine and that’s because of all the factories and stuff around here, so we’re not breathing in the cleanest air,” he said.
“But then a good night’s sleep tonight and I should be okay for tomorrow.”
Donaldson, who leads Ryder Cup stars Peter Hanson and Francesco Molinari by four, had visions of a European Tour first-ever sub-60 round when he birdied the 13th to go to eight under before eventually settling for a new course record of a 10-under-par 62 on the Lake Malaren course.
“I knew I was shooting low but thought after the birdie on 13 that with five to go that a 59 could be on but then I missed the birdie on 14,” said Donaldson.
“It’s crazy because you’re playing the best golf you can and I’ve finished 10-under par but I’m still three off the number.”
McIlroy could understand how the confidence Donaldson gleaned since his four-shot Royal Portrush success has helped him to this point.
“When you win a first event like Jamie did at the Irish Open, it gives you a lot of confidence because I felt like I was knocking on the door for quite a while before my win in Dubai,” he said.
“I had lost a play-off in Hong Kong, finished a shot outside a play-off in South Africa; lost a play-off in Switzerland. So I had close calls. But when you do win it’s more a relief and you get that first one out of the way and you can concentrate on trying to win more.”
Also shooting 67 was victorious Ryder Cup captain Jose Maria Olazabal and Belfast’s Michael Hoey. Hoey had moved to five under par after a dozen holes but stalled with six closing pars as he seeks to move from 61st on the money list and inside the top-60 to qualify for next month’s season-ending Dubai World Championship.
Fellow Irishman Graeme McDowell carded a three-under-par 69, Shane Lowry a level-par 72, Darren Clarke a 74 and Paul McGinley a 74 in the no-cut event.