Stoch flew 245 metres in the first round and 234.5 metres in the second round for a total of 455.6 points.
The Pole's ninth first place of the season confirmed his overall World Cup victory with a total of 1,443 points.
Season runner-up, Germany's Richard Freitag, trailed behind with a total of 1,070 points, followed by Tande with 985 points.
"It was an amazing season, I can't find the right words to describe just what happened, actually," Stoch told public broadcaster TV Slovenija.
After also winning Friday's individual event in Planica, Stoch missed the small crystal globe in ski flying by a total of seven points. He was second overall, behind Andreas Stjernen of Norway (257 points).
Today, the overall World Cup season winner ended 15.5 points ahead of Kraft (243 m, 236 m) and 16 points ahead of Tande (243.5 m, 234.5 m).
Prevc's flights of 235 metres and 232 metres were enough for a total of 424.1 points and a shared eighth place with Norway's Johan Andre Forfang.
"Today is the first day I made all the jumps over 230 metres … It seems that as the season drew to an end, this was the final opportunity to add something [to my jumps]," Prevc said.
But the best Slovenian ski jumper is unhappy with the 15th place overall: "It was a big struggle this season. It was also a struggle last year, but I ended up in ninth place overall … This is the worst season after 2012."
The other three Slovenians competing in today's event, Anže Semenič, Tilen Bartol and Jernej Damjan, were 17th, 18th and 23rd, respectively.
More than 12,500 fans gathered in Planica on Sunday, bringing the total since Thursday to 58,400.