The 28-year-old, on loan at the Valley from Reading, was forced to come off after just 36 minutes.
Manager Alan Pardew told BBC Radio London: "We think he broke his toe and did some ligament damage so he will be struggling to play this campaign."
However, good news for Pardew is that midfielder Lloyd Sam completed 90 minutes for the reserves against Wycombe Wanderers on Monday night.
Also playing in the match was striker Luke Varney, and former Iron defender Kelly Youga.