The 39-year-old police inspector said she felt "on top of the world" after running down Texas-based New Zealander Liza Hunter-Galvan (47) with 5km to go to finish in a time of 3hr 48sec.
Aitken said she was elated with the victory after finishing runner-up twice to Victoria Beck in the race’s first two editions.
"I am on top of the world right now — that is the best feeling, to win this race.
"I thought I might be bridesmaid for a third time but it was my day.
"I have worked so hard for this — it is my first-ever win in a big race. I have a new coach and have trained so hard. I’m just so happy."
Now based in Greymouth as area commander of the West Coast police district, she said her time was slower than expected.
The wind, a cool, gusty westerly that blew in the runners’ faces for much of the course, had been a factor.
Men’s winner Donal Sheehy (36) can now boast a perfect record in the marathon after winning the race on his first attempt at the distance.
The Irishman won in 2hr 39min 39sec, six minutes ahead of five-time Coast to Coast winner Richard Ussher, of Nelson.
Sheehy, whose time was nearly 10 minutes slower than the course record set by Tony Payne last year, broke clear before the halfway mark and controlled the race from then on.
Although an ironman was the nearest thing to a marathon he had raced in before, he knew he was capable of doing well over the distance, Sheehy said.
"I’m looking forward to a few more."
Originally from Dublin but based in Auckland for the past four years, he said it had been a good fortnight for the Irish.
They had beaten the All Blacks, mixed martial arts fighter Conor McGregor had won the UFC lightweight title "and now me winning this".
Ussher (40) said the course was tougher than he anticipated, with frequent changes of gradient keeping him off rhythm.
The Coast to Coast race director, now retired from professional multisport, was also competing in his first marathon.
Coming second was a bonus as he was not as fit as he used to be, he said.
"I keep the expectations in check these days."
Queenstowner Simon Green (40) finished third.
In the half-marathon, the men’s winner was Jason Hall, of Queenstown, in 1hr 12min 22sec, while Hannah Wells, of Te Puke, won the women’s race in 1hr 28min 59sec.
A record 9500 runners took part in the race.
St John Central Otago-Southland Lakes territory acting manager Dianne Payne said a dozen runners were taken to Lakes District Hospital or the Queenstown Medical Centre for treatment.
The most serious case was a runner who suffered concussion in a fall, but the most common issues were minor injuries, dehydration and exhaustion.
A team of 32 staff, including paramedics from Dunedin, Wanaka and Cromwell, covered the course with the help of four ambulances, a motorbike, a quad bike and two "pedal medics" on bicycles.
