The 23-year-old was hurt by Michael's Brown trailing leg as the United midfielder tried to block the ball.
Karacan was lucky to escape serious injury moments earlier in Friday's fiery clash when the Turkish youngster was on the receiving end of a high-footed Danny Pugh lunge that went unpunished by referee Darren Drysdale.
Warnock employed strongarm tactics from the start, with Zac Thompson red carded just 13 minutes in for ploughing into Royals skipper Jobi McAnuff.
If the decision was harsh on Thompson, Brown got away with a string of nasty challenges before the incident which broke Karacan's ankle shortly before half time.
Karacan will see a surgeon on Monday, and Reading boss Brian McDermott said: "I'm really upset for Jem. Some of the tackles did not belong in the game.
"I'm devastated for hm. He's played such a pivotal part in the team."
Royals had to sweat for the victory, with two late Adam Le Fondre goals sealing the win which briefly sent them to the top of the Championship table.
However, they were leapfrogged by Southampton today after their 2-2 draw with Portsmouth and trail the Saints on goal difference.
Reading return to action on Tuesday night when they travel to Brighton, with Hayden Mullins likely to come in for Karacan (7.45pm ko).