The Olympic bronze medallist bested his older sibling in the final metres of a race they dominated, along with Spanish rival Javier Gomez.
It was the first time last year's three Olympic medallists had competed against each other since London and their class showed.
The Brownlees recorded the same 51 minute, five second time while Gomez, who still leads the overall season standings, was nine seconds back to complete the podium.
"I thought it was going to be Alistair's day, I thought I'd never beat him," admitted Jonathan Brownlee.
"He's gone into this pretty unprepared but I knew I had to give everything. I always thought I had a better sprint. I thought if I didn't beat him here I'd probably never beat him."
But his beaten brother admitted he was happy just to be on the podium.
"To be honest, the aim for me was to be in the hunt and I was more than happy to be in it at the last corner. I think I went a bit early," he said.
"I knew I wasn't running that well. I thought I was hanging on for third place, I was hanging on for dear life."
Germany's Anne Haug produced an equally powerful finish to beat Great Britain's Non Stanford and Jodie Stimpson, who won the last two rounds of the series in Madrid and Kitzbuehel respectively, in the women's race.
"I'm absolutely delighted," said Stanford.
"When Annie went she was amazing. I really tried to go with her but didn't have the legs. I was happy to hang on for second."
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- Javier Gomez