Minnaar claimed his second world title and his seventh championship podium with an impressive run to edge out Great Britain's 2008 world champion Gee Atherton while favourite Aaron Gwin (USA) was never a threat after suffering a mechanical problem.
The French were favoured to dominate the women's title but it was a surprise in the form of Morgane Charre who prevailed over favourite and compatriot Emmeline Ragot.
Auckland's Sophie-Marie Bethell and Nelson's Veronique Sandler finished 24th and 26th respectively in the elite women's competition.
Earlier Coatesville teenager Sophie Tyas placed eighth in the junior women's contest while the best of the junior men was Takaka's Reece Potter who was 18th.
Potter, who slipped his pedal out of the start hut, said the changing conditions were difficult to prepare for after slippery, wet and muddy conditions for practice.
"I missed the first jump after slipping my pedal but after that the run was okay," Potter said. "With the conditions getting drier and rougher, we actually had problems through the forest section with the morning sun making it difficult to see.
"We had not practiced in those conditions so it was difficult to judge, and tyre choice was important."
Tyas said she was a little disappointed with her run but motivated to move up to the elite ranks next year.
The action moves to nearby Saalfelden in Austria for this week's cross country world championships which begin on Friday (NZ time).
Results:
Elite men: Greg Minnaar (RSA) 3:21.790, 1; Gee Atherton (GBR) 3:22.371, 2; Steve Smith (CAN) 3:23.004, 3. Also New Zealanders: Brook MacDonald (Napier, MS Mondraker) 3:26.651, 8; Sam Blenkinsop (Wanganui, Lapierre International) 3:28.165, 11; Cameron Cole (Christchurch, Lapierre International) 3:29.073, 16; Justin Leov (Dunedin, Trek World Racing) 3:30.324, 21; George Brannigan (Havelock North, DeVinci Global) 3:30.855, 26.
Elite women: Morgane Charre (FRA) 3:50.654, 1; Emmeline Ragot (FRA) 3:51.853, 2; Manon Carpenter (GBR) 3:52.144, 3. Also New Zealanders: Sophie-Marie Bethell (Auckland) 4:23.113, 24; Veronique Sandler (Nelson) 4:24.778, 26.
Elite junior women: Holly Feniak (CAN) 4:01.622, 1; Tahnee Seagrave (GBR) 4:09.717, 2; Danielle Beecroft (AUS) 4:19.567, 3. Also: Sophie Tyas (Auckland, NZL) 4:32.541, 8.
Elite junior men: Loic Bruni (FRA) 3:29.139, 1; Richard Rude (USA) 3:32.260, 2; Connor Fearson (AUS) 3:34.083, 3. Also New Zealanders: Reece Potter (Takaka) 3:42.449, 18; Louis Hamilton (Rotorua) 3:48.204, 34; Leo Sandler (Nelson) 3:48.506, 35; Lawrence Cawte (Rotorua) 3:51.632, 43; Dan McCombie (Dunedin) 4:01.728, 60.