Footage taking by radio DJ Roman Kemp, who is at the match, showed fans in Barnsley shirts running out of the stadium - with their side 3-1 up and only seconds to go.
He tweeted: "Millwall fans broken through police barrier and Barnsley fans now running to other stands."
Several videos taken from fans inside the stadium showed supporters exiting the ground as people in Millwall shirts ran towards them.
Rob Summerfield tweeted: "It's a sad occasion for Millwall so they're holding a minutes's violence."
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