One of the most dramatic finishes in triathlon history featured Jonny initially coasting to the win of the men’s elite race.
But then he started to succumb to the fierce heat that has marked the worlds in Cozumel, Mexico.
First Brownlee staggered and then slumped to the ground.
Alistair abandoned his duel with South African Henri Schoeman to help his younger brother.
Schoeman won the race and Jonny was second, with Alistair alongside him for third.
There was a protest against the Brownlees’ finish, but under triathlon rules assistance from other competitors is allowed.
Jonny needed medical attention afterwards and the result cost him the world series title.
Had he held on, Jonny would have taken the series lead from Spaniard Mario Mola.
But Mola finished fifth and that was enough to secure the overall series win.
Schoeman won the 1.5km swim, 40km cycle and 10km race in an hour 46 minutes 50 seconds, with the Brownlees crossing the line 18 seconds later.
Alistair beat Jonny a month ago to win his second-straight Olympic triathlon gold medal.
Ryan Bailie, who finished 10th in Rio, was the only Australian to finish in the top 10 at Cozumel with a sixth placing.
Fellow Rio Olympian Aaron Royle was 16th and Glasgow Commonwealth Games competitor Dan Wilson ended his international career with 22nd.
Cozumel was also the retirement race for two-time world champion Emma Moffatt, who did not finish.
Compatriot Charlotte McShane won bronze in the women’s elite race.
Flora Duffy of Bermuda beat Rio gold medallist Gwen Jorgensen and that also gave her the women’s series title.