The 2013 Masters champion from Australia was four under par after 13 holes, playing some wonderfully controlled golf in the late afternoon sunshine.
Scott was three under after just five holes and reache the turn at four under. He bogeyed the 12th, but got back to four under with a birdie at the next.
McIlroy had earlier set the standard in the clubhouse with a six-under 66 which gave him a one stroke lead over Italy’s Matteo Manassero.
Two more Italians – the Molinari brothers Edoardo and Francesco – were a further stroke back at four under, level with Americans Jim Furyk and Brooks Koepka and Sergio Garcia of Spain.
Eight players were grouped on three under 69 including Tiger Woods who opened with two bogeys but had three birdies in a row from the 11th hole.
Defending champion Phil Mickelson was one over par after 11 holes, but playing partner and 2012 champion Ernie Els was a disastrous eight over after hitting a young spectator with his first tee shot.
World number three Justin Rose was one under after 11 and US Open champion Martin Kaymer one over through 15.