Adam Le Fondre, signed from Rochdale for £150,000, forced home a low Paul Warne cross with a flying diving header in the 24th minute.
Then in the 37th minute Tom Pope, signed from Crewe for a similar fee, rose above the defence to power home a strong downward header.
Macclesfield were given a lifeline when Matthew Tipton crashed home his third of the season with a pinpoint half volley to convert a Colin Daniel cross.
Tipton was making amends for what turned out to be a crucial miss in the eighth minute when after being fed by Reneil Sappleton he sent a one-on-one chance past the keeper but also inches past the upright.
But the Millers sealed the game in the 88th minute when midfielder Danny Harrison swept home a low shot from 15 yards.