Barré, who made a solo breakaway over the final 14 kilometres, finished 10 seconds ahead of Scaroni and Germany's Marco Brenner in the 125.5 km mountain stage starting and finishing in the southern mountain resort of Bukowina Tatrzańska.
Poland's Filip Gruszczyński finished 23rd, 36 seconds behind Barré, while former Tour de Pologne winner Michał Kwiatkowski finished more than 7 minutes behind the winner.
Scaroni leads Barré by 3 seconds in the overall standings, with former leader Bart Lemmen of the Netherlands a further two seconds back.
Gruszczyński is 23rd overall, 1 minute and 52 seconds behind the leader.
The race will be decided on Sunday in an individual time trial in the southern town of Wieliczka.
At least 10 riders remain in contention for a place on the podium, Polish state news agency PAP reported.
Italian cyclist Christian Scaroni (right) finished second in Bukowina Tatrzańska on Saturday to claim the yellow jersey. Photo: PAP/Grzegorz Momot
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Source: TVP Sport, PAP