The 20-year-old MS Mondraker Team professional took out the men's downhill title in Val d'Isere to break the winning streak of American Aaron Gwin (Trek World Racing), who had won four rounds straight this year.
It follows from the victory of Wanganui's Sam Blenkinsop in the downhill World Cup in Austria four years ago.
"I can't even explain in words at the moment how I feel," said Macdonald on Redbull.tv after winning. "I had a solid run with no mistakes. It was just one of those runs. I'm over the moon.
"I struggled all this season and I was at the point where I was hating riding. I changed a few things on my bike, like the suspension set up, and it paid off. This track was hard with the altitude and being 2.5 minutes. You're pushing the whole way and you can't lose time.
"I think I'm going party for a week."
Gee Atherton (GT Racing) finished second, 0.68 seconds behind Macdonald while Josh Bryceland (Santa Cruz Syndicate) was third. Minnaar (Santa Cruz Syndicate) and Gwin rounded out the top five.
MacDonald, the 2009 junior world champion, had to cope with a deteriorating track which made his run all the more meritorious. He was sixth after the first split and first at the second split to take the win.
He said he had a smooth run and while pushing hard, he kept within his limits and this proved a key to his breakthrough victory.
The victory bumped MacDonald up to eighth on the World Cup standings with one round remaining.
MacDonald became the first rider other than Gwin or Minnaar to win a World Cup in 2011 and 2012.