Beck (29) felt a bit underdone going into the event, having been through an "intense time" recently with university exams.
"This is a bit of a surprise," she said after the race.
"I figured Shireen [Crumpton] and Vanessa [Harverd] would be favoured ahead of me."
Beck had targeted a time under 6hr for the event and was relying on her base fitness level to get her through the 60km mountain run, and bank the day's work as part of her build-up for the Hong Kong marathon in February.
Beck led for the first 9km on the 13.5km uphill stage to Luxmore Hut, but was then overtaken by defending champion Crumpton and Harverd, last year's runner-up.
She caught up with Crumpton again on the ridgeline, with Crumpton beginning to suffer from an ankle condition she took into the race. It ultimately led to her withdrawing from the event around the halfway point.
Feeling a second wind kick in from what she described as a "brutal" uphill section to Luxmore Hut, Beck overtook Harverd on the downhill, and opened up a decisive gap on the long valley section to the finish.
For no apparent reason, apart perhaps from her lack of preparation for the race, Beck took a couple of tumbles along the way, crossing the finish bloodied and bruised in 5hr 51min 28sec.
Harverd, the open women's champion in 2009 and one of the Australian entrants, clinched second place for the second consecutive year in 6hr 8min 3sec, with Queenstown's Sarah Coghlan third in 6hr 13min 2sec.
Beck, better known on the international duathlon stage, has decided to concentrate solely on her running during the next few years while she completes her orthodontic studies.
She has already had an impact, finishing eighth in this year's Hong Kong marathon in 2hr 45min and runner-up in the Rotorua marathon which doubled as the New Zealand championships in April.
Defending Kepler Challenge men's champion Vajin Armstrong (31) broke free from the threat posed by three-time champion Martin Lukes (40) at Luxmore Hut and powered his way to the finish in 5hr 1min 54sec.
The Christchurch duo appeared to have made it a two-man race on the 13.5km run up to Luxmore Hut, until Armstrong hit his straps, motivated by the thoughts of all his family and supporters.
Armstrong's turn of pace left Lukes with the runner-up medal for a fifth time in 5hr 9min 3sec. Third was Wellington's Daniel Clendon (35) in 5hr 17min 46sec.
In the associated 27km Luxmore Grunt, it came down to a battle of the generations, with Stuart Doyle (45), from Canberra, getting the jump on the youth of Winton's Troy McAlister (17) only over the final stages.
Doyle completed the course in 2hr 2min 43sec and McAlister, tiring a little on the run home, finished second in 2hr 4min 17sec. Third was Richard Ford in 2hr 10min 47sec.
Wanaka's Jess Simpson won the open women's section in 2hr 18min 39sec from Australians Claire Corbett and Beth Cardelli.
