The 20-year-old was replaced by Aaron Sinclair just half an hour into Saturday's Irn-Bru First Division clash after a lunge from Bairns defender Ryan McGeever left him crocked and unable to continue.
Bannigan is now on crutches and will wear a protective boot in the coming weeks as he faces a lengthy spell on the sidelines.
The news will come as a huge blow to Bannigan and Firhill boss Jackie McNamara, with the youngster turning in a number of superb performances this season.
The injury to one of the Jags' key men topped off a disappointing 0-0 draw for the Firhill side as they saw Dunfermline leapfrog them back into pole position in the title race.
It was perhaps understandable that Falkirk manager Steven Pressley set his side out to stifle Thistle's free-flowing forward line but midfielder Sean Welsh admits he was surprised by the Bairns' approach, with a share of the spoils leaving them 12 points off the promotion pace.
"It was a bit frustrating. I think they parked the bus a bit and especially in the first half when they just sat in," he said.
"It was hard for us as we aren't used to coming up against that.
"We thought that it would be quite an open match but they just sat in and looked quite happy to try and catch us on the counter attack.
"Second half we were able to put them under a bit more pressure but obviously they were dangerous on the counter attack with the pace that they have.
"I've always known Falkirk as a footballing side that come at you. So we were surprised that they sat in and kept 10 men behind the ball, especially with them at home.
"That's the way that their manager set them out to play but it is still hard for us to play against that. I suppose with us playing so well then we're going to come up against that more often.
"Teams are a bit wary of us. We've scored a lot of goals this season, teams are sitting in and trying to catch us on the counter attack. It is a compliment, but it is up to us to try and break these teams down."
Next up for the Jags is a clash with Highland League side Cove Rangers as they kick off their William Hill Scottish Cup campaign.
McNamara's side have already booked their place in the Rams-dens Cup final, where they will meet Queen of the South in the spring, and Welsh is keen for a run in Scotland's top knockout competition.
He said: "It will be different. I don't know what to expect from them but I think it will be a hard game for us. We'll need to make sure that we prepare correctly and have our minds ready for the game.
"It's the Scottish Cup and we want to go as far as we can in it and get a cup run going. We will be ready for next week's game when it comes."