The 83rd-minute spot-kick was all the home side had to show for a dominant performance in which only Mazembe goalkeeper Sylvain Gbohouo stood between Sundowns and a runaway score.
The Ivory Coast international goalkeeper pulled off a host of brilliant stops to keep his side in the game until full back Issam Mpeko was penalised for a wild lunge on Sundowns captain Hlompho Kekana and Brazil-born Nascimento stepped up to convert.
Sundowns winger Anthony Laffor had three close-range efforts saved by Gbohouo while a series of other chances also went begging.
It was Sundowns' first triumph in the African Super Cup -- an annual one-off game between the winners of the continent's two major club competitions, the Champions League and the African Confederation Cup -- having won the Champions League for the first time in October.
(Reporting by Mark Gleeson; Editing by Neville Dalton)
