After landing awkwardly on an offensive rebound, Whiteside limped off the floor and immediately underwent X-rays, which came back negative. Whiteside will undergo an MRI Sunday to determine if there is ligament damage.
Whiteside was asked after the Raptors' 95-91 win if this could be a long-term injury.
"I don't know. We'll know more when I get the MRI," he said, according to the Miami Herald. "I'm going to just pray on it."
The Raptors also lost their starting center for the remainder of Game 3 as Jonas Valanciunas suffered a sprained right ankle in the third quarter.
Whiteside had been hampered by a right knee strain after another awkward landing in Game 1 on Tuesday and had to be removed from the game. He returned shortly afterward and logged 39 minutes in the overtime victory. In the Heat's Game 2 overtime loss, Whiteside played 39 minutes again, marking the first time in his career that he had played at least 36 minutes in consecutive games.
Whiteside scored six points before leaving Saturday's game with the Heat trailing 25-19. The 26-year-old has posted a team-high 24.0 player efficiency rating this postseason, leading all players with 110 rebounds.
"Guys have to step up," Heat guard Dwyane Wade said."Nobody can be Hassan Whiteside. ... We have to figure out a way."
The Heat center will be an unrestricted free agent this summer after spending the past two seasons with the Heat and finishing third in this season's NBA Defensive Player of the Year vote behind San Antonio Spurs forward Kawhi Leonard and Golden State Warriors big man Draymond Green.
The Whiteside injury comes on the heels of the Heat announcing on Wednesday that big man Chris Bosh will miss the remainder of the postseason after being sidelined with an unspecific medical condition since February.