Wesley Said's late goal earned Dijon a fifth win in seven Ligue 1 games as Malcom's stunner was in vain for Bordeaux.
Jonathan Cafu scored the opener after Alexandre Mendy's effort was cleared off the line, but ex-Bordeaux man Cedric Yambere headed home Xeka's corner to equalise.
Just two minutes after that, though, Malcom restored the visitors' lead in some style. The 20-year-old Brazilian cut in from the right and, from 35 yards, sent a ferocious left-footed drive swirling into the far top corner with goalkeeper Baptiste Reynet a helpless spectator.
Xeka forced a sharp save from Benoit Costil early in the second half and Dijon were level moments later when Said crossed low for Benjamin Jeannot to sidefoot home from close range.
Julio Tavares was denied a penalty after being barged in the back by Bordeaux's Jeremy Toulalan but there was a late winner for Dijon as impressive substitute Valentin Rosier's through-ball found its way to Said, who curled home a neat first-time finish.