The Hatters were awarded a penalty, to the surprise of everyone on the pitch, in the 68th minute as Jordan Hadfield was judged to have fouled Asa Hall. Tom Craddock stepped up to blast home his tenth of the season and give the hosts back-to-back league wins for the first time this campaign.
Luton started the game in positive fashion and created the first chance 10 minutes in when Kevin Nicholls' corner picked out Michael Spillane on the edge of the area and from the defender's instant volley Mark Bower fired the ball over the bar from eight yards.
The Hatters pressed against the massed ranks of visiting defenders with little to show for their efforts and Macclesfield tried their luck on the break.
In the 26th minute John Rooney, brother of Wayne, tried a speculative 40-yard lob after home goalkeeper Dean Brill had made a rushed clearance, but the ball dropped over the crossbar.
The visitors went even closer in the 31st minute when a long throw into the home penalty area caused panic in the Luton defence and the ball fell for Nat Brown to power a 10-yard volley that smashed the crossbar and flew away.
Luton again dominated possession and in the 40th minute they made Jon Brain work, as he pushed the ball around the post from Keith Keane's 25-yard effort. From the resulting Nicholls' corner Brain then, under pressure, punched the ball against his own crossbar and behind for another corner.
Macclesfield came out the brighter in the second period and Gareth Evans ended a 30-yard run with a 20-yard effort straight at Brill in the 55th minute. Matthew Flynn headed the ball against a post two minutes later, but the effort wouldn't have stood anyway as he was flagged offside.
Mick Harford reshuffled on the hour, replacing Sam Parkin with Ian Henderson and eight minutes later the hosts were ahead in dubious circumstances.
Craddock's jinking run took him the byline and from his cross, Hall appeared to miss the ball, but instead - to both teams' surprise - a penalty was awarded for a foul by Hadfield. Craddock duly stepped up to blast the ball home for his tenth goal of the season.