The 27-year-old won the Four Hills opener in Oberstdorf on Sunday but it looked liked he would be off the podium after a less than impressive first-round leap placed him ninth overall.
However it didn’t prove costly at all as Jacobsen’s second-round effort of 143m, 0.5m off Simon Ammann’s hill record, promoted him all the way to first and denied Gregor Schlierenzauer once again.
Jacobsen, who took a year out from ski jumping last season, took his points total from 128.4 to 277.7 with defending champion Schlierenzauer scoring 276.8 overall in Germany.
Anders Bardal beat off competition from Norwegian teammate Tom Hilde to take third by 0.8 points as Four Hills leader Jacobsen refuses to get ahead of himself with two rounds two go.
“It was not in my mind to extend my lead,” said Jacobsen, who with all four rounds of the Four Hills Tournament acting as World Cups denied Schlierenzauer a 44th career win.
“I knew I could have good jump despite the problem with my skis in first round and in the end it was a perfect second round.”
Much like the head-to-head knockout first round in Oberstdorf, there was an early casualty in Garmisch-Partenkirchen in the form of Wolfgang Loitzl.
Loitzl, the Four Hills champion from 2009, lost to Germany’s Maximilian Mechler and didn’t advance while Lukas Hlava fall’s paved the way for Matjaz Pungertar.
Kamil Stoch produced clear the best leap of round one with his effort of 142m just 1.5m off Ammann’s hill record but that didn’t produce the best score.
Stoch scored 134.3 points to tie second overall with Hilde as Austrian Schlierenzauer impressed the judges most after jumping 134m for 137.1.
Jacobsen, who won the Four Hills opener in Oberstdorf , was almost a high-profile casualty himself after a severely disrupted flight phase.
The Norwegian recovered to beat Andreas Kofler and progress to the second round as an outright winner but ninth looked to have put him out of contention.
It didn’t though as Jacobsen came out firing in the second round as Norway’s ski jumpers came to the fore to dramatically alter the top three.
Schlierenzauer went from first to second and Stoch joint second to sixth with reigning world Cup champion Bardal moving up from fifth to third.