Tyrone Van Aswegen overcame a double-bogey and a bogey by reeling off 10 birdies, including two chip-ins, for a day's best seven-under 65 to trail Armour by a stroke.
Vaughn Taylor shot 66 to sit two back on a day when 30 players failed to complete the round before a series of afternoon thunderstorms halted play for the day.
Irishman Seamus Power was best placed, two shots behind with two holes left.
Armour once took Tiger Woods to 19 holes in the final of the 1993 U.S. Amateur Championship, but as professionals their careers went in different directions.
While Woods went on to win 14 major championships, Armour has never finished better than fourth in 104 starts on the PGA Tour, and only once before has enjoyed the 36-hole lead.
"I love it, that's why we play," he said of being out front.
He was thankful to negotiate his back nine in even par after some wayward drives.
"I drove it in the rough a little bit on that side, so getting away with some pars I feel blessed," he said.
"The speed of the greens got away from me a little bit too, and I kept being one or two revolutions short on the birdie putts."
Second-placed Van Aswegen said the key to his 65 had been maintaining a positive attitude after dropping two shots at his seventh hole.
"After that double I made it was basically a decision to just carry on and keep going because if you hang your shoulders your round is probably toast," said Johannesburg-born Van Aswegen, who became a U.S. citizen in 2013.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Peter Rutherford)
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