The Northern Irishman, searching for his first major championship, entered the round tied for first and picked up steam as the day progressed, ending 54 holes solidly ahead at 12-under 204.
McIlroy birdied three holes on the back nine to establish a strong hold on the lead.
Former Masters champion Angel Cabrera registered a 5-under 67 Saturday to forge a tie for second place at 8-under 208 with Charl Schwartzel (68), K.J. Choi (71) and Jason Day (72).
Four-time Masters winner Tiger Woods, meanwhile, had a rough day after charging into contention with a 66 in Friday's second round. Woods stumbled to 2-over 74, falling into a ninth-place tie at minus-5.
Anther Masters winner, Phil Mickelson, carded a 1-under 71 en route to a 3-under 213, good for 18th place.