McAuley was left unmarked to head home Kevin Sandwith's free-kick in an even but scrappy first half.
The Imps dominated after the break with Macclesfield keeper Alan Fettis saving Derek Asamoah's turned-in shot while Simon Yeo flashed the ball just wide.
Matthew Tipton went closest for Macclesfield, hitting the bar with a long-range effort in the first half.
Macclesfield manager Brian Horton:
"We are still in with a great chance going to our place. We already beat them at ours," said Horton.
"They're strong, they did a magnificent job. We knew they'd be a handful and they scored from a set-piece.
"They play three up front and take a chance and they do it well, and it is all set up for an exciting second leg."
Lincoln City: Marriott, McCombe, Morgan, Futcher, McAuley, Butcher, Gain, Sandwith, Asamoah, Taylor-Fletcher, Yeo.
Subs Not Used: Beevers, Bloomer, Hanlon, Frecklington, Ryan.
Goals: McAuley 11.
Macclesfield: Fettis, Bailey, Swailes, Barras, Morley, Harsley, Carragher, Whitaker (Townson 78), McIntyre, Parkin, Tipton.
Subs Not Used: Wilson, Miles, Briscoe, MacKenzie.
Ref: G Laws (Tyne & Wear).