Burton, who went top for the first time in their 58-year history last week, stayed in top spot after victory at the leagues bottom side.
The first half had 15 minutes' injury time after Burton's Tony James injured his head and Lewes's Ollie Rowland was taken off in a leg brace.
The goal came in stoppage time, when Aswad Thomas felled Lee Morris and Greg Pearson duly converted the penalty.
Shaun Harrad nearly made it 2-0 but hit the bat from the edge of the box.
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Booked: Gargan, Cullip.
Burton Albion: Poole, Buxton, James (Austin 24), Webster, Simpson, Gilroy, Pearson (Banim 80), McGrath, Corbett, Morris (Harrad 68), Newby. Subs Not Used: Deeney, Bailey.
Goals: Pearson 45 pen.
Att: 630
Ref: K Yeo (Essex).
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