Reid was the second athlete eliminated, having expended all of his energy fighting for team points.
“I'm absolutely gutted,” he said.
“I got eliminated last week, and I said I never want to feel like that again, and to get that again just really, really hurts.”
Although he didn't want to make excuses, Reid said he knew he wouldn't be on race pace after being unwell in the week before the event.
“I wasn't 100 percent, but I wanted to do my best for the team. I knew if I gave it everything, I could get some points in the swim.”
Often Olympic triathlons are decided in the run at the end, while the Super League Triathlon series uses an alternative race format that changes slightly every weekend to find the best triathlete in the world.
Competitors work in teams and as individuals over four races on as many weekends with $1.25 million in prize money.
In Munich, the athletes did two laps of the course on the bike in a time trial format before a staggered start into two back-to-back sprint triathlons where anyone falling 45 seconds behind the leader at any transition was eliminated.
Reid sits 19th on the Super League series leaderboard after the first two events. Fellow New Zealander and team member Hayden Wilde slipped back from the top spot after winning the opening leg in London, settling into fourth place after finishing fourth in Munich.
The series heads to Jersey in the United Kingdom this weekend before wrapping up in the sunshine of California's Malibu the following week.