Leading with 700m left, Jonny, 26, began to weave over the road in hot and humid conditions in Cozumel.
Third-placed Alistair, 28, caught his brother, propping him up for the final couple of hundred metres before pushing him over the line in second place.
They were overtaken by South African Henri Schoeman, the eventual winner.
Victory in Mexico would have given Jonny the world title, but second place left him just four points behind Mario Mola.
The Spaniard was fifth on Sunday to top the overall standings.
Jonny, Olympic silver medallist at Rio 2016 and a bronze medallist at London 2012, collapsed to the ground the moment he crossed the finish line.
He required treatment but later tweeted he was OK, with a photo of himself lying in a hospital bed on a drip.
Alongside a video clip of the finish of the race, the 2012 world champion also wrote: “Normally when you have had too much to drink. This time it was the opposite #ouch”