Firhill chairman David Beattie announced the move last night and said: "The consequences of incendiary devices in a wooden-clad stand are there for all to see."
Thistle took the controversial decision to ensure they received a Safety Certificate for the ground ahead of their return to Scotland's top flight next season.
Fears over flares had prompted authorities to review the matter and the decision has now been taken to give Celtic fans the North Stand.
The agreement comes just weeks after trouble marred the Glasgow Cup Final at Firhill when fans set off flares and smoke bombs.
Beattie added: "The Police Football Intelligence Unit raised concerns as to the increased use of flares by sections of some away support, citing a number of incidents that have taken place over the last season.
"This, along with our own experiences of flares at Firhill over the last couple of seasons, meant it is something we have to seriously consider."
A Jags 'singing section' was situated in the North Stand last season, but the group will have to be moved when Celtic travel across Glasgow to accommodate the Hoops fans. Beattie said: "At the club's Operations Board Meeting, it was agreed that approaches would be made to representatives from the North Stand to keep them up to speed.
"But due to people's commitments the original meeting date was delayed.
"Unfortunately, events overtook that consultation process as the timings around the renewal of the Safety Certificate meant that a strict segregation policy which banned Celtic supporters from the main stand was enforced.
"In essence, this left the club with a fait accompli regards moving our own fans."
While Thistle have been left with little option but to relocate their supporters for the Celtic clashes, the decision will infuriate Jags fans who revelled in the North Stand last season.
The red and yellow army played their part in Thistle's First Division title success by roaring Alan Archibald's side on from the stand, but will now have to be moved from their usual seats for one of the biggest matches of the campaign.
Beattie said: "We share our fans' frustrations that due to elements outwith our own control we are required to move our fans from the North Stand.
"However, we are confident that no matter their location, the Thistle fans will provide the players with fantastic support and again make us proud of our wonderful fans."
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