The 36-year-old surged with 200 meters to go and hung on to reach the finish ahead of Italian Luca Paolini and Dutchman Max Van Heeswijk.
Paolini retained the overall leader's jersey after the 212 km ride from Ostroda to Bydgoszcz.
"It was the kind of finish I like. There was a small climb and the wind was blowing against us," said Kirsipuu who clinched his 122nd professional success and eighth in the Tour of Poland.
"I decided to stay behind Max van Heeswijk and to follow his pace. With 200 metres to go I made my move and I passed him," said a smiling Kirsipuu.
"It's good to win .............
again as my preparation during the winter break was weak. I did everything wrong. But since the Tour de France I feel much better," he said.
As in the previous two stages, the peloton was not eager to hurry things up and the average speed was just above 30 kph when they began chasing Spaniard Jose Julia who broke away early.
Julia's lead went up to 21 minutes but the Illes Balears rider used up too much energy in his solitary surge and was caught a few kilometers from home.
The fourth stage from Inowroclaw to Leszno over 214 km of flat roads should see another massive sprint finish.
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