A 10 minute spell in the sin bin for Brantham keeper Matt Walker proved pivotal as the Imps lost 3-1 at homes, after being in front.
Brantham were looking good after taking the lead from Asa Millard but George Bugg equalised for Mildenhall.
The Imps could have gone in front when Jose Santa De la Paz picked himself up to take a penalty after bing fouled in the box but hit a post.
The game swung Mildenhall's way when Walker was sin-binned by referee Alex Shipp for showing dissent while arguing over controversial penalty decision.
Walker was booked for the mould and then sent to the sin-bin for 10 minutes, rather than being shown a second yellow and a red.
Staff Millardo went in goal but was beaten by Daryl Oakley from the spot.
Millardo was beaten again from a well-struck Bugg shot and even when Walker came back on and it was 11 v 11, Brantham could not rally sufficiently.
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