The 27-year-old won the first two rounds of the Four Hills Tournament at the end of December and start of January before relinquishing the overall lead to defending champion Gregor Schlierenzauer.
Jacobsen was 15th in his first outing since in Wisla on Wednesday however he was back among the winners as the World Cup circuit travelled across Poland to Zakopane.
He won with an overall total of 273.3 with defending World Cup champion Bardal second with 271.6 and home hope Kamil Stoch down in third with 268.7.
Stoch actually led after round one, the Pole one of three to jump 133m but awarded the best score, 141.2, while Jacobsen was second with 137.8 after a leap of 128.5m.
And as Stoch fell after jumping 127m second time out Jacobsen went from second to first and Bardal from fifth to second with the biggest leap of the round.
Jacobsen's effort of 131.5m put the pressure on Stoch who couldn't do enough to hold on to first place while Bardal's leap of 132m was responsible for his rise.
Schlierenzauer was eighth but still leads the overall World Cup standings with 840 points with Bardal way off in second with 655 and Jacobsen third with 578.
