The German recorded two fine jumps with his 134.0m effort in round two securing the win in tricky conditions on the Malinka hill.
Team-mate Karl Geiger took second ahead of Austria's Daniel Huber, with first-round leader Anze Lanisek slipping to sixth place.
Reigning normal hill Olympic champion Andreas Wellinger was 39th on his return to action having missed the whole of last season with a knee cruciate ligament tear.
"It was a little bit windy after the table but it was quite a good jump too... The landing is always terrible, but my second World Cup win, it's unbelievable. I'm so happy." - Markus Eisenbichler to FIS
Consistency wins the day for Eisenbichler
After strong winds prompted the cancellation of the trial round, organisers deemed conditions safe enough for the competition to get underway.
The gusts meant jumpers were subject to significant wind compensation deductions, and made for something of a lottery as to when their coaches would signal for them to set off.
Two of these in the thick of the action in yesterday's team competition were to the fore in the first round.
Eisenbichler went out to 137.5m to score 130.9 points.
Then Huber, who made a huge contribution to Austria's victory over Germany on Saturday, went even further with 138.5m - just 0.5m shy of Kraft's hill record - to amass 133.4 points.
But it was Anze Lanisek who held the lead at the halfway stage.
The Slovenian clearly likes the Malinka hill, finishing second to Tande 12 months ago for his best individual World Cup finish to date.
He only jumped 136.0m but received high style marks to top the leaderboard with 134.6 points.
Geiger was fourth at the midway point and matched his first-round score of 129.3 to go into the lead.
Then came Eisenbichler who had a bit of a wobble mid-air before going big again and just holding on to his landing.
HIs distance of 134.0m yielded a score of 136.7 points for a formidable 267.6 total.
Huber was next to go and could not match his first-round heroics, flying 125.5m to tally 255.7 points and take him into third.
Lanisek also failed to rise to the occasion with his jump of 118.0m seeing him drop to sixth place.
That saw 29-year-old Eisenbichler secure his second individual World Cup victory having broken his duck on the Planica ski flying hill in March 2019.
A month before that, he had his first big international success on the large hill at the World Championships in Innsbruck.