Alistair became the first triathlete to retain an Olympic title in Rio as he led his brother.
The brothers, who finished first and third in London, did not put a foot wrong in front of packed crowds on Copacabana.
It came down to a race between them and Alistair made his break on the third lap of the run, pulling away to claim a dominant victory.
Jonny comfortably held on for silver, making the brothers the first to finish one and two at an Olympics since Italians Piero and Raimondo D’Inzeo in equestrian in 1960.
Alistair picked up British and Yorkshire flags 100 metres or so from the finish and sauntered down the finishing straight, at one point stopping and holding his arms aloft before crossing the line.
The final gap to Jonny was six seconds, with Henri Schoeman taking bronze for South Africa.
The start of the race went exactly to plan for the Brownlees, who finished the 1.5 kilometre swim in the waters off Copacabana in fourth and sixth place and immediately pushed the pace on the bike.
With eight laps up and down a brutally steep hill, the course played into the hands of the Yorkshiremen, who train in the Dales.
Big dangers Mario Mola and Fernando Alarza of Spain missed the front group of 10, as did Richard Murray of South Africa, and the gap soon began to grow.
It has not been a smooth four years for Alistair since London, with injuries an all too frequent problem, and last summer he took the decision to have ankle surgery.
The gamble paid off and he moved back into his customary position at the top of the world by dominating races in his home city of Leeds and Stockholm earlier this summer.
His biggest rival, Javier Gomez of Spain, the silver medallist in London and a five-time world champion, was expected to be the big danger again but he was forced to miss Rio after fracturing his elbow in a training fall.
It was tough to see where the challenge to the Brownlees was going to come from, so perfectly had their race plan played out.
Gordon Benson, the third member of the British team, was picked to support the Brownlees but, having failed to make the front group, he had to sit in the pack and avoid helping the chase and he dropped out on the penultimate lap.
At the start of the 10km run along the beach front, the gap was a minute and 14 seconds.
By the time the chasers arrived at transition, the Brownlees and France’s Vincent Luis had already made a break for it.
But Luis could not stay with them for long and paid for his early efforts as he was overtaken by Schoeman.