Pajari languished in third after suffering a puncture on Friday morning, but fought hard to seize the lead of the category two stages later.
From that moment on, the Finn remained unchallenged as several of his rivals hit trouble over the following days.
A clean drive over Sunday’s final leg secured Pajari’s second victory of the year by 5min 40.2sec.
“It has been really difficult,” said Pajari. “Even now on the last stage, I was not pushing, but there was a small bump that surprised me a bit.
“Okay, we have finished a very tough rally and it looks quite good. I really need to be satisfied with this win,” he added.
Lauri Joona was second. He dropped time with a puncture on Saturday’s Amarante test and was never really close enough to put any pressure on Pajari.
Mcrae Kimathi completed the all M-Sport Poland Ford Fiesta Rally3 leaderboard. The young Kenyan restarted on Sunday morning having retired on both the previous two days.