Donaldson moved to 12 under despite a mixed round that featured an eagle, four birdies and three bogeys. The Welshman is one shot ahead of England's Anthony Wall, with Padraig Harrington and Mark Foster another shot back at 10 under.
McIlroy improved 13 spots to tie for 11th with a 71, while France's Gregory Bourdy toppled from the leaderboard with an 80.
McIlroy started with two birdies in his first three holes, but bogeyed No. 5. He then ran off 13 straight pars.
"I've struggled on the greens all week," the Northern Irishman said.
McIlroy has missed the cut in four of his last five tournaments and lost his No. 1 ranking to Luke Donald. He used a new driver in hopes of changing his luck.
"I think it's going to make a big difference," McIlroy said of his new club. "It puts less spin on the ball, which is just great in the wind, and it goes 15 yards farther."
Bourdy went from a one-shot lead at the start of the round to eight behind with six bogeys, a double and a triple-bogey 8 to tumble out of contention.
Inspired by a first career hole-in-one on Thursday, Donaldson was on course to break his European Tour title drought after recovering from a bogey on his first to push just ahead of Wall.
"I've had a few chances, but at the end of the day I've not been good enough so far to stand on the last green holding the trophy," the 36-year-old Donaldson said.
Harrington shot a 72, but the 2007 champion was still in contention.