In his only event of the Games, the 20-year-old looked to send it in his second qualification run, knowing that while his 69.25 had him in 10th after the first run, he would likely need to improve on it to make the top 12 and move on to the final.
Things started well in his run, but after appearing to lose a little speed on landing one of his tricks, Harrington didn't hit the next lip of the halfpipe as he needed to and was left flailing in mid-air before gravity took hold.
Harrington appeared to smack his head and neck against the lip and he ricocheted on to the flat ground in the middle of the pipe.
The 20-year-old stayed down for a couple of minutes while he was attended to by medical staff, as the silent crowd watched on.
Fellow Kiwi Miguel Porteous was one of those onlookers holding their breath.
"That was one of the gnarliest crashes I've ever seen in the pipe and for it to be one of your teammates, your heart just sinks to see that," Porteous told Sky Sport.
Finally, a warm applause rang out as Harrington got back to his feet and gestured to the crowd - saying "thank you everyone; thank you everyone for watching" as he walked past, before emotion took over when his score came in - a 23.50.
"I'm OK, I'm just bummed," Harrington told Sky Sport after his run. "That last run was going great, I just fell at the end. I'm just happy I'm healthy and getting to ski with all these amazing skiers.
"Everything was feeling good, I guess that's just how the ball rolls some times; it's just part of life."
To compound the disappointment of falling on his last trick, Harrington's first run score saw him finish in 13th place - one spot out of the finals.
New Zealand will have two athletes competing in the final, with the Porteous brothers, Nico and Miguel, finishing in second and ninth respectively.
Fellow Kiwi Gustav Legnavsky, just 16 years old, finished qualification in 19th place and was also affected by Harrington's crash.
"That last run... all I could think about was Benny and hoping he was okay and really wanting to make him proud," he told Sky Sport.
The final for the event is scheduled to take place on Saturday afternoon from 2:30pm.
