Adding to the misery of the weather, Thompson suffered a fall coming off the Cargill walkway, about 3km from the finish line, and was later diagnosed with two broken bones in his arm.
Thompson (32), a physiotherapy clinical adviser, made his first appearance on the course since winning the event in 2005.
''That was cold, muddy and hard,'' he said after crossing the finish of the 26km race over the peaks of Flagstaff, Swampy and Mt Cargill.
''That was the coldest run I've ever had.''
Thompson, who is returning to the sport after three years as a ranked distance runner that culminated in him winning the national marathon title in 2007, has found renewed enthusiasm for running after a break for family and work commitments.
A brief move to Australia after his 2007 national marathon success was backed up with victories in the Townsville marathon and Mt Isa half-marathon, before he returned to Dunedin and gave the shoes a rest.
His approach to training is completely different from what it was six years ago. He now works his training around family before going for late-evening runs, and is enjoying a much more relaxed approach.
''I just do it for fun now. I don't take it too seriously.''
This approach saw him feeling ''really strong after the start'', and deciding to go with it. He reached the top of Flagstaff in 56min and held a 3min lead at Swampy.
Thompson continued to distance himself from the remainder of the field, overcoming a wind chill that plummeted temperatures into the negative on his run over Mt Cargill, before getting some respite on the run down to Bethunes Gully and the finish at Chingford Park.
He crossed in a time of 2hr 6min 53sec, well clear of second-placed Phil Novis (2hr 15min 34sec) and Otago marathon champion Jason Palmer (2hr 19min 52sec).
''Stafford was just flying up those hills,'' Palmer said afterwards ''Unfortunately for me, there are no hills in Balclutha.''
Defending champion Louisa Andrew dominated the field to retain the women's title in 2hr 33min 43sec.
''That was tough,'' Andrew said at the finish.
''But I'd rather have that than the 34degC we had on the Peninsula Challenge a couple of years ago.''
Andrew (39), a horse dentist, has build a remarkable record for off-road running.
''I just enjoy running this course. You never know what it's going to throw up.''
Second in the women's section was Tamsyn Hayes in 2hr 45min 52sec, while in third place was Thompson's wife, Bridget, in 2hr 47min 50sec.
