A last-gasp header by defender Peter Murphy earned Carlisle a narrow advantage to take into the second leg of the LDV Vans Northern Area Final.
Andy Smart had earlier snatched a shock lead for the Silkmen with a stunning 22-yard snap-shot.
But the home side grabbed an equaliser through top scorer Karl Hawley after he was set up by Chris Lumsdon.
Stand-in skipper Murphy then rose unchallenged to meet Simon Hackney's right-wing corner from six yards.
Carlisle: Westwood, Arnison, Livesey, Murphy, Aranalde, Rivers (Hackney 55), Billy, Lumsdon, Adam Murray, Holmes (Glenn Murray 68), Hawley.
Subs Not Used: Williams, McGill, Grand.
Goals: Hawley 20, Murphy 90.
Macclesfield: Lee, Teague, Morley, Swailes, Harsley, Whitaker, Smart, McIntyre, Sandwith, Wijnhard, Bullock.
Subs Not Used: Bailey, Miles, Beresford, Briscoe, Deasy.
Goals: Smart 9.
Ref: N Miller (Co Durham).