The Finn started on the back foot after puncturing a tyre on SS3, but he fought hard to reclimb the order and seized the lead three stages later when early pacesetter Jon Armstrong retired with damaged rear suspension.
From that moment on, Pajari remained unchallenged as several of his rivals hit trouble over the following days.
He carried a near six minute advantage into the final day and eventually won the M-Sport Poland Ford Fiesta Rally3 category by 5min 40.2sec, taking home maximum points following disappointments in Sweden and Croatia.
“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.
Robert Virves completed the podium, although the Estonian finished nearly 20min further back after suffering seven flat tyres over the course of the event.
Armstrong managed to salvage eight Wolf stage win points after restarting on Saturday morning to claim fourth. Kenyan driver Mcrae Kimathi was fifth after crashing on Friday and stopping with mechanical gremlins on Saturday.
William Creighton’s fraught weekend came to a head on the first pass of Fafe. The Motorsport Ireland Rally Academy youngster was unable to continue after hitting a banking and damaging his car’s rear suspension.