Due to strong side winds, the final round of Sunday's World Cup in Planica had to be cancelled, leaving the results decided according to the first round jump scores.
That meant Kraft took top honours having recorded by far the longest jump of the day with 250m to score 244.3 points.
Second went to Andreas Wellinger of Germany on 236.2 points after a jump of 238.5m while Japan's Noriaki Kasai was third on 223.9 points.
Victory made it eight World Cup wins this season for 23-year-old Kraft, who also clinched two individual golds, mixed team silver and team bronze at this year's World Championships. He said:
It was another unbelievable day. Being on top of the podium three times was too much for me. For the first time ever I started crying at a ceremony. I want to thank my team and the ski jumping family. It's special to be a part of it. Thanks to all of you.
After 26 individual competitions this winter, Kraft wins the overall World Cup title for the first time in his career with 1665 points, 131 ahead of Four Hills Tournament winner Kamil Stoch of Poland with Daniel Andre Tandre of Norway in third on 1201 points.
Stoch's Poland did clinch the Nations Cup though with 5833 points ahead of Austria on 5586 and Germany on 5513.
Kraft also finished top of the Ski Flying World Cup standings on 445 points, followed by Wellinger on 333 and Stoch 279.
Read the original article on Eurosport: Kraft revels in maiden overall World Cup title