Christchurch rider Cameron Cole (Lapierre International) also enjoyed an outstanding run to finish sixth yesterday, with MacDonald (MS Mondraker) 14th. Cole's teammate Sam Blenkinsop (Wanganui) recovered from a fall to finish 41st, Takaka's Reece Potter pushed the Kiwi-designed Zerode bike into the top 50 while Wellington's Richard Leacock finished 59th.
Auckland's Sophiemarie Bethell finished 16th in her first world cup final, with Nelson's Veronique Sandler 19th.
Brannigan had a measured start, only 12th quickest through the first time split but he claimed the top spot in the Hot Seat as fastest with a lightning run through the rest of the course to clock 3:32.164.
His DeVinci Global teammate Smith then tore through the opening big jump section nearly two seconds faster than the Kiwi and while he lost time to Brannigan through the rest of the course, the Canadian held on to claim the victory in 3:31.764.
"I am pretty stoked," Brannigan said. "It is definite relief to be up there. This season my main aim was consistency after last year, just being in the top 20.
"This race I wanted to hold it open and get a really good result. It feels like a long time coming.
"My contract is up but I have no reason not to sign with DeVinci again. It is an awesome team and we all get on well."
The Hawkes Bay rider says he will ease back into riding over the New Zealand summer.
"The main focus when I get home will just be to enjoy riding, even through the summer series and after the nationals I will really step it up in training and try to come into the season really strong next year."
MacDonald has been the Kiwi standout this season with four top-10 finishes capped off with his victory at Val D'Isere.
"To tell the truth I found this week hard. I was really over it and looking forward to going home," MacDonald said.
"It wasn't the weekend I wanted but I'm seventh overall and I am happy with my season.
"I will have a couple of months off the bike and chilling, then getting back into it and race the national series.
"My contract is up so it will be an interesting time with some hard decisions to be made."
Cole also capped off a strong season after coming back from serious injury that sidelined him for six months, finishing 11th overall in the world cup standings.
"I had a really good day. The track was amazing. Conditions were quite fast and it flowed really well."
Like Brannigan's and MacDonald's, Cole's contract is up for negotiations.
"I have been talking to some people and have some plans next year.
"I am really looking forward to coming home injury-free to work through our summer towards next year."
He said the week had been stressful after news of the death of close friend and mentor James Dodds.
"I wanted to pay my respects to Dodsy. He gave me drive this week and I've realised what this life is all about - having fun for me and being able to ride my bike in all these amazing places is pretty cool.
"It's been a hard week and to pull a good ride together for him was great."
