On a rainy night at Don Valley, Rotherham were pegged back after taking a first half lead but took the spoils in the final ten minutes to go level on points with rivals and weekend opponents Notts County, who drew with Bradford.
The Millers started the brighter of the sides and took a deserved lead on ten minures, as the ball broke to Danny Harrison on the edge of the area.
The midfielder fired home a well struck 20 yard skidder which beat keeper Brain into the bottom corner.
Adam Le Fondre then had a shot blocked, as the Millers continued to press with Brain somehow keeping out a Gavin Gunning header from Nicky Law's assist.
The Millers were pegged back though as the Silkmen responded with almost their first attack to stun the home crowd, as Ben Wright poked home Craig Lindfield's through ball after an initial shot had been blocked by Ian Sharps.
With Dale Tonge being replaced due to injury by Mark Lynch, the visitors set up camp for a point after the restart but almost caught the Millers square on the break as Pablo Mills produced a superb last ditch tackle on Wright after he was fed by Lee Bell.
Abdulai Bell-Baggie was introduced for Josh Walker and Drewe Broughton entered the fray, but it took until 12 minutes from time for Le Fondre to restore the lead, converting a penalty after he was kicked on the by line after hitting the deck under an initial challenge.
Ref Salisbury consulted his linesman before pointing to the spot and Alf made no mistake for his 27th of the season.
Just two minutes later the tension in the 2,900 crowd was eased as Broughton smashed home the rebound after Bell-Baggie's shot was tipped away.
The three points leaves Rotherham handily placed ahead of Saturdays crunch trip to Meadow Lane.