Two weeks after a breakthrough first career WRC win in Estonia, Pajari and co-driver Marko Salminen finished 26.7 seconds ahead of teammate Oliver Solberg, who was the joint top Sunday scorer with nine points from the final day.
It was also the 200th WRC win by a Finnish driver, coming in the 75th edition of an event that started out as the 1,000 Lakes Rally in 1951.
"It was a big thing to take the win in Estonia, but a home win is always something special," said Pajari, who inherited the lead on Saturday when teammate and reigning world champion Sebastien Ogier crashed out while comfortably ahead.
"Winning at home has not been so easy for the Finns but after one really crazy rally we made it."
Championship leader Elfyn Evans completed a podium sweep for Toyota, whose team is headquartered in the central Finnish city of Jyvaskyla that hosts the rally, and won the final Power Stage for bonus points.
The Welshman, who rolled his car on Saturday, extended his overall lead after 10 of 14 rounds to 30 points over Pajari, who moved up to second with Japan's Takamoto Katsuta dropping to third and 41 points behind Evans.
"More than anything, we owe thanks to the guys who fixed the car yesterday lunchtime," Evans said.
Hyundai's Adrien Fourmaux and Thierry Neuville were fourth and fifth with Toyota's Katsuta sixth after hitting a tree on the final stage.
"I was trying to avoid a rock on the inside," the Japanese explained after finishing with a heavily damaged car. "What a disaster weekend."
Irish driver Josh McErlean was seventh for M-Sport Ford and Toyota's Jari-Matti Latvala eighth.
Evans now has 201 points to Pajari's 171 with Katsuta on 160 and Solberg 156. Ogier, who was cleared after hospital checks, is on 139.
In the manufacturers' standings, Toyota lead with 514 points to Hyundai's 340. The next round is in Paraguay from August 27 to 30.