The Olympic silver medallist went down early in the bike leg in slippery conditions while leading and, although he did not lose too much time, his right knee bore the scars of the crash.
It was clear from the start of the run that Brownlee would not be in contention for a podium place and he eventually crossed the line 53 seconds behind South African winner Henri Schoeman.
Schoeman, the bronze medallist behind both Brownlee brothers in Rio in 2016, recently faced allegations that he failed a doping test during the Olympics, but the International Triathlon Union cleared him of any wrongdoing.
Schoeman is likely to provide the main opposition to both Brownlee brothers - Olympic champion Alistair missed the race in Abu Dhabi with a calf injury - at the Commonwealth Games in Australia next month.
Jonny has also targeted a second world title to add to the one he won in 2012 but this was not the start he would have wanted.
Meanwhile, Wetherby’s Jess Learmonth finished second in the women’s opening race i as the Netherlands’ Rachel Klamer won gold.
South Africa’s Natalie Van Coevorden took bronze as several athletes, including world champion Flora Duffy, crashed out in the wet conditions on the sprint-distance course. “It was carnage,” said Learmonth. “I’m really pleased. I’ve done well here but there is still a month to go until the Commonwealth Games.
“It gives me a bit of confidence and we’ll have to see what it brings.”
Compatriots Vicki Holland finished 11th, former world champion Non Stanford 16th and Sophie Coldwell 26th.