Trouble broke out in the section housing supporters of the Championship outfit during the second half, with trouble escalating following the Latics' second goal.
A 43-year-old man was charged with racially aggravated behaviour while another 53-year-old was charged with breaching bail conditions.
The former will appear before Hendon magistrates on May 1.
Detective Chief Inspector Andy Barnes said in a statement: "The violence seen at the Millwall v Wigan FA Cup fixture over the weekend is completely unacceptable.
"A significant investigation is now under way to identify all involved in order to bring them to justice in a swift and robust manner."
The Football Association have described the events as "unacceptable" while Sports minister Hugh Robertson condemned the scenes as "incredibly disappointing and depressing".
Millwall chief Andy Ambler insists the club are "determined" to see justice brought to the fans who brawled in the stands at Wembley.