The right-back has enjoyed a solid season for Alan Archibald's side but will play no further part in their battle to beat the drop from the SPFL Premiership in the coming weeks.
Thistle have not had their injury problems to seek this term, with boss Archibald deprived of the services of midfield duo Sean Welsh and Isaac Osbourne for several months now.
Defender Conrad Balatoni missed last weekend's 4-2 defeat by Hearts due to a hand knock.
And now the Jags, who will face Kilmarnock in their first post-split fixture next Saturday, have been rocked by O'Donnell's injury- enforced absence.
Archibald said: "It has been more or less things as usual this week.
"We have picked up a lot of injuries recently unfortunately and it is hard to work the players too hard because we are down to the bare bones at the moment.
"Stephen is going in for an operation on a hip problem and that will be him out for the rest of the season.
"Hopefully, he will be back for pre-season.
"You don't want to be playing guys when they are not fit and you don't want to have to play players out of position either.
"While we wanted another game coming off a bad result against Hearts last weekend, the break has probably come at a good time for us as it lets the lads get over a few of the knocks."