Kajetanowicz came into the final round with a comfortable lead over Irishman Breen - who has struggled with reliability all season in his Peugeot 208 T16 R5.
The Pole secured the win when the event - which had been marred by poor conditions - ended after only six of the scheduled nine stages were run as organisers decided the heavy rain made it too dangerous to continue.
Ford Fiesta R5 driver Kajetanowicz has managed three wins this season - the same number as Breen - but a consistent run of results from the 36-year-old allowed him to overturn Breen's big early lead and then pull away.
The Acropolis victory gave him an insurmountable 68-point margin over Breen with the season finale in Valais still to run.
"It's an amazing feeling. It was the most difficult day of my life," said Kajetanowicz.
"Everything is finally perfect and beautiful."
Breen was left frustrated by the early finish to the event.
He was 10 seconds behind at the time, but had been leading by half a minute before having to slow when his bonnet flew open and blocked his vision on what turned out to be the final stage.
"Stupid weather, it was a disaster, but nobody can do anything about it," he said.
"I don't know if it was the right decision to cancel the rest of the stages because I was not there.
"It's a disappointing decision but there is nothing I can do about it."
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