The 44km race between the Remarkables Ski Area and Coronet Peak Ski Area comprised a 2km snowboard/ski down the Remarkables, a 17km downhill mountain bike, a 7km paddle on Lake Wakatipu, a 9km run and a 9km uphill road bike.
Mason led the individual men's race for the first three legs before Allan overtook him at the beginning of the fourth stage.
Most of the field, including Milne, were diverted to an early exit at the Queenstown Gardens and took a big lead on the men's field in the run.
Allan and Mason chased hard and Allan finally overtook Milne with about 500m to go on the uphill slog to the Coronet Peak base building.
He claimed the men's trophy for the third time in 2hr 20min 52 sec, just 1min ahead of Milne. Mason was third in 2hr 27min 38sec.
Maier, the defending women's champion, was less than four minutes behind Mason and finished fourth in 2hr 31min 08sec.
She shaved six minutes off her own course record and finished the first two stages - a 2km downhill snowboard/ski and 17km downhill mountain bike - hard on Mason's heels.
Former winner Joanna Williams, of Wanaka, was second woman in 2hr 40 min and also took several minutes off her fastest time.