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An MRI scan on his injured left hamstring has revealed a strain, the team announced.
In more dire injury news for Golden State, backup center Kevon Looney has a non-displaced collarbone fracture and is out indefinitely.
Both Thompson and Looney were injured during the Warriors' 109-104 win over the Raptors on Monday in Toronto, a result that leveled the best-of-seven series at one win apiece.
The Warriors travelled to Oakland, following game two but didn't arrive until after 4am local time, delaying Thompson's MRI and Looney's MRI and CT scan until later in the day.
The team initially announced that Looney had a chest contusion, but coach Steve Kerr later said that Looney's injury was "something with his shoulder."
Thompson got hurt in the fourth quarter Monday. He said after the game he expected to play in game three tomorrow, though he was seen limping around Scotiabank Arena following Golden State's win.
Kerr said postgame, "Klay said he'll be fine, but Klay could be half-dead and he would say he would be fine."
The Warriors continue to await the return of All-NBA forward Kevin Durant, who will miss game three.
He hasn't played since sustaining a right calf injury in game five of the Western Conference semifinals nearly a month ago.