Docherty had an idea that something different was in store when he saw the media mobbing Armstrong the day before in the race briefing and tweeted afterwards: "Hopefully it's not like that on the bike tomorrow otherwise we're screwed."
Docherty was third after the 2km swim and seventh after the non-drafting 90km bike leg, which he was surprised Armstrong didn't dominate.
"I thought Lance would absolutely cream us on the bike but he was probably in a similar position to me where he wasn't too sure how to pace himself. He certainly looked like he was holding back and that was probably why he ran so well off the bike."
Docherty quickly made up ground on the 21km run but passed Armstrong with only 2.5km remaining and won by half a minute.
"It's great that I could hold one up for the other triathletes and show that it's certainly not a sport that you can just walk into and dominate straight away," he said. "It's quite an honour to see a seven-time Tour de France winner and someone you admire standing in second place below you on the podium. It's a highlight of my career."
The ultra-competitive Armstrong, who began his sporting career as a triathlete before concentrating on cycling and won seven Tours de France after surviving cancer, has long been a high-profile and polarising figure. The US Government last week decided Armstrong would not be charged after a two-year probe into accusations that he and his teammates systematically used performance-enhancing drugs to prepare for races.
Docherty decided only two weeks ago to compete in the race and said it would serve as an important base in his bid to qualify for the Olympics in August. He won silver in Athens in 2004 and bronze in Beijing four years later and hopes to gain selection for a swansong in London.
While Armstrong is new to the event, it was only Docherty's second half ironman. His first was in France 12 years ago in which he took the lead in the last 100m of the race.
Dramatic, but not as controversial as today.
Results: Bevan Docherty (NZL) 3:50:13, 1; Lance Armstrong (USA) 3:50:55, 2; Richie Cunningham (AUS) 3:52:59, 3.