Gareth McAuley's 11th-minute goal means it is advantage Lincoln after the first leg of the semi-final play-offs.
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.
