The British Open runner-up posted a 13-under 127 total, while consistent Englishman Justin Rose shot 63 to roar into second place on 11-under.
McIlroy and Woods, who shared the first round lead, could not maintain their torrid pace.
McIlroy plodded to a 69 to fall four strokes behind, while Woods (70) bogeyed the final two holes to slip five back.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Ken Ferris)
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