Warren was stretchered off two minutes before half-time following a heavy challenge from Motherwell defender Stephen Pearson, who received a yellow card.
Thistle’s stand-in skipper, deputising for Richie Foran, was taken to hospital for tests and the club confirmed the news on their official Twitter feed.
“We can confirm that, unfortunately, Gary Warren’s injury from yesterday is a break,” Inverness tweeted on Sunday.
“We’ll update on the prognosis when we know more.”
Inverness manager John Hughes also lost Josh Meekings to an injury but he maintains he will not be able to add defensive cover to his squad.
The only defensive cover Inverness have brought in this summer is Nat Wedderburn, who can play at the back or in midfield, but he was sacrificed in the first half for debutant Andrea Mbuyi-Mutombo.
Wes Fletcher’s fourth-minute goal ensured the points would be returning to Fir Park but it was the injuries, particularly to Warren, that put a further black mark on the game.
Jordan Roberts, Carl Tremarco and James Vincent were already ruled out, while Aaron Doran and Foran were not present in the match-day squad.
But recruiting to cover the gaps is not an option, insists Hughes.
“We haven’t got the budget. We’ve got players that are adaptable and can play in a number of positions, with one or two that we need to get up to speed,” he said.
“There isn’t the money to bring anyone else in so we’re just hoping to get one or two back.”