Brownlee pulled out during the running stage of the event on medical grounds with what looked like a stomach problem.
He was clearly struggling and at one point was picked up by TV cameras clutching his midriff shortly before retiring less than halfway through the 10km run.
This was the third staging of the event in Leeds and with his younger brother Alistair ruled out of the race owing to hip injury, Jonny would have fancied his chances of securing an elusive win on the city’s roads.
The 28-year-old secured two runner-up spots in the past two stagings in the city and would have been dreaming of sealing top spot in a race that he holds so dear.
However, Brownlee entered this race on the back of so-so form and had said beforehand that he was “not in an amazing condition, but a very good condition”.
He was forced to drop out after clearly showing signs of struggling.
The swim in Roundhay Park was a testing one with the sun beating down on the participants, and Brownlee exited the water just 11 seconds behind early pace-setter Richard Varga.
Brownlee made a swift transition from water to bike and was initially bunched in the front cluster that made its way towards the city centre.
At one point the congested group held a 34-second lead over the chasing pack as they headed towards the seven laps that weaved their way around the middle of Leeds.
But as the tight roads took their toll on the pack that lead was slowly eaten away.
Brownlee dropped further back as the final few laps of the bike section approached and came in 59 seconds behind the leader Richard Murray at T2.
Brownlee was clearly struggling and less than halfway through the 10km run he withdrew to head to the medical tent.
South African Murray was charging forward relatively unopposed and held a 13-second advantage heading into the final lap before sealing victory with a time of 01:45:53.
Murray said the victory was unexpected following a poor run of form. “I can’t explain it really,” Murray said.
“I’ve had a really tough time over the past three months. I’ve worked really hard and this is my first Olympic distance win.
“Now that I’ve finally done it I’m really, really happy.
“I love racing in the UK and the last time I did was in London when I came second, so I definitely enjoy racing here.”
In the women’s race another hometown favourite Jessica Learmonth had to make do with eighth place.
Learmonth could not last the pace as Vicky Holland stormed to a surprise comeback win.
Olympic bronze medallist Holland, who lives and trains in Leeds, outgunned her rivals to secure her first World Series victory since 2015.
Learmonth said she struggled with the final leg following a gruelling swim and cycle.
“I could hardly walk, never mind run for 10km,” she said. “This course just doesn’t let up. It’s a really, really hard course and you should be really proud if you do well here. It could have been better for me, but overall I’d say I’m still happy with a top-10 finish.”
Learmonth impressed in the swim and initially surged in front before forming part of a breakaway pack. She was sandwiched between American pair Taylor Spivey and Katie Zaferes and the trio proceeded to build a gap of 58 seconds between themselves and the rest of the field.
But the unforgiving West Yorkshire roads saw that advantage eventually trimmed when the rest of the field, including Holland, clawed back some valuable time as they meandered through the streets of Leeds and towards the city centre.
The second transition saw Learmonth lose the ascendancy completely and it was then Holland who took the race by the scruff of the neck in the final leg to seal a terrific result.
A confident display saw her finish in 01:56:32 – 17 seconds clear of fellow Briton Georgia Taylor-Brown.
Holland said: “(Yesterday) was brutal and I think I won in the ugliest way possible.
“Somehow I’m standing here with a gold medal and I’m over the moon about it.”
Leeds-based Non Stanford pulled out of the race after falling ill just hours before.
Stanford, 29, took to social media to inform her followers that she was undergoing tests in hospital.
She said: “Nothing serious I hope and sure to see you all soon.”