Shane Lowry and Giles Coke were sent off following the flashpoint, which occurred late in the Championship contest, while Stephen Bywater and Atdhe Nuhiu received yellow cards.
The FA confirmed the charges for both clubs on Thursday.
"Both Millwall and Sheffield Wednesday have been charged by The FA for failing to ensure their players conducted themselves in an orderly fashion and/or refrained from provocative behaviour," read a statement on the organisation's official website.
"The charge relates to an incident in or around the 88th minute of their match on Tuesday (28 January 2014). The clubs have until 6pm on 3 February 2014 to respond to the charge."
Coke had given Wednesday the lead after 69 minutes, in Stuart Gray's first game as permanent manager, before DJ Campbell equalised on his debut for Millwall.
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