Farrell joins teammate and fellow halfback Dan Houston (suspension) on the sidelines for the finals in another blow to Port's defensive stocks.
Houston has served one match of his five-game ban, while Farrell hurt his left hamstring in Port's away win against Fremantle on Sunday.
The 93-gamer's precision left-foot kicking was instrumental in Port finishing the home-and-away season in second spot to set up a home qualifying final against Geelong on September 5.
But scans confirmed "a high-grade hamstring strain, with the defender to be sidelined for the rest of the season", Port said in a statement on Tuesday.
Farrell and Houston have been key components of Port's defence, which is ranked third in the competition for points conceded behind the Western Bulldogs and Brisbane.
"As a backline, we've all got to step up," fellow defender Logan Evans told reporters on Tuesday.
"It's not just one person taking a massive step, it's everyone taking a few steps forward and being able to cover the roles all together and as a cohesive group."
Eight-gamer Josh Sinn looms as a likely replacement for Farrell, while key forward Todd Marshall will be available for the Adelaide Oval qualifying final against the Cats after completing his mandatory 12-day spell after being concussed.
Evans earned an AFL Rising Star nomination for his performance against Fremantle when the 18-year-old collected a career-high 23 disposals.
AFL Rising Star nominee Logan Evans (left) will be a key part of Port Adelaide's defence. (Michael Errey/AAP PHOTOS)
Plucked by the Power in the mid-season draft, Evans has played 10 consecutive games since making his debut in round 16 against the Brisbane Lions.
The backman has trained with Port since January under an SANFL rookie program after being overlooked in last year's national draft.
"It (being overlooked) made me want it more," Evans said.
"I just had to work even harder because I didn't get picked up and it was disappointing, but there was no point in putting myself back in my shell ... (I just had to) step out of my comfort zone and keep doing the work.
"I got to go to Port at the start of the year with the rookie program, so that was a massive step for me, just being in this environment, seeing what it took and then trying to match it.
"Life has just gone pretty quick, it has been a pretty full-on and surreal three or four months."
In injury news elsewhere, Western Bulldogs gun Adam Treloar will have to prove his fitness for next Friday's elimination final against Hawthorn as he deals with a calf issue.
The Bulldogs said Treloar had felt some calf tightness in the warm-up of Sunday's win over GWS, but had got through the game and would be freshened up this week.
Laitham Vandermeer has avoided a serious hamstring injury but will be racing the clock to play while Jason Johannisen is primed to return after overcoming a lingering calf injury.
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