The FA's independent regulatory commission will decide West Ham's punishment on Friday after finding the club guilty of two charges: failure to ensure their supporters refrained from violent, threatening, obscene and provocative behaviour, and failure to ensure their supporters did not enter the field of play.
West Ham face a range of possible sanctions including being forced to play games behind closed doors and a heavy fine.
The violent clashes led to 64 arrests and the stabbing of a Millwall fan outside Upton Park, and there were pitch invasions during the match.
The FA said in a statement: "An independent regulatory commission last week heard charges issued as a result of the serious crowd disturbances in and around the West Ham United versus Millwall fixture at Upton Park on 25 August 2009.
"It was alleged that both clubs failed to ensure that their supporters conducted themselves in an orderly fashion.
"The independent regulatory commission, chaired by an independent QC, found West Ham United to be in breach of FA rules in the following respects: failure to ensure their supporters refrained from violent, threatening, obscene and provocative behaviour; failure to ensure their supporters did not enter the field of play.
"The commission will reconvene this Friday (15 January) to consider the issue of sanctions.
"The commission found all charges against Millwall not proven.
"The FA will now await the full written reasons from the independent commission before making any further comment."
Millwall chief executive Andy Ambler said the decision vindicated the club's vigorous defence against the charges.
Ambler told the club's website: "Millwall FC welcomes the verdict in respect of our club as we have always maintained that we were innocent of the charges.
"As ever this club condemns all misbehaviour within football stadia and works tirelessly to eradicate misconduct and to continue to change an unfair and distorted misconception of Millwall Football Club and its fans.
"We thank the FA Commission panel for their judgement and we will make no further comment until we receive and consider their full statement on the matter, which we anticipate will be on Friday."
West Ham confirmed they had been cleared of two of the four charges initially brought against them by the FA but said they were unable to comment further until the disciplinary process had been completed.
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