Pearce was playing his first match since injuring his calf against Carlton but was subbed out in the opening minutes of the first term.
"Unfortunately he's nicked his Achilles tendon and he'll play no further part in the year," Lyon said on 6PR.
Garrick Ibbotson has also been battling Achilles soreness and has missed the past five weeks. Lyon says he is struggling to be fit for Saturday's qualifying final against Geelong.
"They're two that have been critical to us," Lyon said.
"So that leaves a big hole in our back six.
"Luke McPharlin will be declared fit as long as he has no hiccups this week and then we just have to make a decision whether he plays or not."
McPharlin has not played since tearing his calf in round 15 against St Kilda.
Lyon said Nick Suban, Stephen Hill and Michael Walters have all overcome issues to be available to face the Cats.
Fremantle rested Nathan Fyfe, Hayden Ballantyne, Michael Johnson, Chris Mayne, Zac Clarke, David Mundy, Lee Spurr and Zac Dawson but Lyon believed all would come back into the line up.
