One of the men was charged with racially aggravated behaviour, while another has been charged with breach of bail conditions.
Three other men have accepted cautions and five have been released with no further action.
A total of 14 fans were arrested after numerous fights broke out in the end reserved for Lions supporters during the match on Saturday, which Wigan won 2-0.
Detective Chief Inspector Andy Barnes said: "The violence seen at the Millwall v Wigan FA Cup fixture over the weekend is completely unacceptable.
"The Metropolitan Police is committed to working with its partners in bringing those responsible to justice.
"A significant investigation is now under way to identify all involved in order to bring them to justice in a swift and robust manner."
Scotland Yard added that a 24-year-old man from the Camberwell area of south London was bailed to return to a north west London police station after being arrested on suspicion of theft, possession of a Class B drug and possession of an offensive weapon.
A 15-year-old boy, from Croydon, south London, was arrested on suspicion of ticket touting. He was bailed to return to speak to police in early May.
Scotland Yard said officers were pursuing numerous leads as part of their post-match review and will continue their probe to identify those involved.
Millwall have been working with the Football Association and police to try and identify those responsible.
Lions chief executive Andy Ambler discussed the issue with FA chairman David Bernstein and general secretary Alex Horne on Monday.
Saturday's violence, which saw Millwall fans attacking police and fighting among themselves inside and outside the ground, was followed by more trouble in Sunday's Tyne-Wear derby in which Sunderland beat Newcastle 3-0.
Northumbria Police are studying CCTV footage after Newcastle fans battled on the streets outside St James' Park.
Twenty-nine people were arrested but that number is expected to grow as police continue their investigations.
Meanwhile, British Transport Police made 33 other football-related arrests over the weekend.
Offences included violence and racist abuse during a number of outbreaks of disorder, including fans of Chelsea and Manchester City returning from Wembley's second FA Cup semi-final on Sunday.