However, the young Canadian rode spectacularly well at the final three events and, with just 17 points separating the pair before the final race, Smith swooped to take home the title.
Atherton remains the world number one downhill rider and, with Smith missing the first race in Pietermaritzburg through injury, he will be targeting a repeat of his opening day win 12 months ago.
But the 29-year-old admits that he will be up against one of the closest fields the event has ever seen in 2014 – but winning is still the only thing on his mind.
“The goal is always to win,” he said. “Of course Stevie Smith is going to be top of everybody's mind because of how last season panned out for both of us.
“It's important not to get focused on what any one other rider is doing but every year since I’ve been racing World Cups a new crop of talent has come through and upset the expected order.
“I don't expect this year to be any different.”
With Friday’s qualifying done and dusted some of those riders are already suggesting they will be challenging for World Cup podiums this season.
American Aaron Gwin, who claimed back-to-back titles in 2011 and 2012 but struggled last year, is top of the pile going into today’s finals. Greg Minnaar looked strong on his home track to finish third while 19-year-old Loic Bruni also impressed.
2010 World Cup Series Champion Atherton finished slightly off the pace in 15th but knows better than anyone that, in downhill racing, every fraction of a second counts and anything can happen in the finals.
“These days in the men's race it always comes down to tenths or even hundredths of seconds,” he added.
“That's how we've spent the winter, looking for every hundredth of a second that we can save.
“The preparations for this season have gone really well. I’m super excited to get stuck in at Pietermaritzburg.”
There may be plenty of competition on the men’s circuit to occupy Atherton but there is also a well-known sibling rivalry in Team Atherton.
The Welsh rider shared podiums with his sister Rachel last season as she went on to win the women’s World Cup and tipped her and the rest of his teammates to achieve more success in 2014.
“The mood is amazing in the team,” he said. “Everyone is stoked to have Taylor (Vernon) back on the bike and Martin (Maes) is now a fully integrated, English-speaking, Enduro-ass-kicking member of the team.
“Everyone's riding really well and the support team we have are all over it. It feels like they can all achieve whatever they set their minds to.”