Kobayashi was fourth at the halfway stage, and that was where he finished with Karl Geiger moving ahead of Kubacki into second.
Lindvik had the shortest jump of the top four in round two, but the 21-year-old had more than enough in hand to claim victory by 4.8 points and truly make his name in the senior ranks.
"I struggled a bit yesterday to find out the hill, but today I really found out what I needed to do and I'm so happy." - Marius Lindvik to FIS Ski Jumping
Weather hinders Kobayashi quest
After sweeping all four of last season's Four Hills events, Kobayashi made it five wins in a row at Oberstdorf on Sunday (29 December) to match the record held by Nagano 1998 Olympic champion Kazuyoshi Funaki.
But his bid to break the tie with his compatriot was hampered by Mother Nature as the calm conditions which greeted the earlier jumpers in round one gave way to a slight cross and tailwind.
Lindvik, who was only 35th in Tuesday qualifying, had taken full advantage of those conditions with his score of 147.7 points leaving him well clear of his rivals.
Kubacki also enjoyed the still, jumping 137.0m for 140.2 points and second place.
In contrast, Kobayashi - third in qualification - managed 132.0m, 11.5m behind Lindvik, as he scored 137.7 points to go third.
Top qualifier Karl Geiger, runner-up to Kobayashi at his home hill Oberstdorf, also scaled 132.0m but his score of 138.7 points saw him send the Japanese down to fourth.
Daiki Ito set the target in round two with a jump of 136.5m to move up from ninth place.
He held that lead until the defending champion took to the hill again.
Kobayashi produced an excellent effort of 141.0m to go into the lead, but he was quickly overtaken by Geiger who has emerged as his main rival this season.
Seeking Germany's first success at Garmisch since Sven Hannawald's Grand Slam season of 2002, Geiger leapt 141.5m to go into the lead and end Kobayashi's history bid.
He stayed in front as PyeongChang 2018 team bronze medallist Kubacki went out to 139.5m to move ahead of the Japanese.
That left just Lindvik to go and it was the youngster's turn to be disadvantaged by a tailwind.
It did not bother him, however, as his jump of 136.0m and wind compensation saw him come out on top by nearly five points with a total score of 289.8.
Kobayashi stays ahead in the Four Hills tournament but his lead over Geiger has been reduced to just 6.3 points.
The fliers head to Austria for the remaining two events with Innsbruck hosting the third event on Saturday (4 January).