Ten people were arrested after violence erupted in the Millwall supporters area at Wembley Stadium in the second half as Wigan beat the second-tier club 2-0.
The images of bloodied fans brawling being beamed around the world revived memories of Millwall's problem with hooliganism in the 1970s and 80s, and prompted the London club to pledge to ban any guilty fans from its games for life.
"There are always a few idiots," said John Berylson, the American who owns Millwall. "That's not our fan-base and we don't even know who those people are. We will be investigating."
Wigan's victory was secured by Shaun Maloney's crisp volley in the 25th minute, and Callum McManaman netting from a tight angle in the 78th.
Wigan was taking a break from its struggle for Premier League survival, with it remains in the relegation zone.
In league action on Saturday, Arsenal came from behind to beat Norwich 3-1 to climb a point above Chelsea and Tottenham into third. Chelsea has a game in hand.
Everton strengthened its grip on sixth place and plunged Queens Park Rangers closer to relegation by winning 2-0, while bottom-place Reading held Liverpool 0-0.
Wigan, which is also in the drop zone, is playing Millwall on Saturday in the FA Cup, and Chelsea faces Manchester City in the other semifinal at Wembley Stadium on Sunday.
City's season hinges on cup success, with Manchester United 12 points in front at the top of the standings.
Arsenal's priority is finishing in the four Champions League spots, and now has qualification back in its hands.
Early in the second half, it appeared Arsenal would remain in fifth when slack defending allowed Michael Turner to rise to meet a free kick from Robert Snodgrass.
Manager Arsene Wenger responded with a double change, with Theo Walcott and Lukas Podolski replacing the returning Jack Wilshere and Gervinho.
It took until the 85th to pay off, with Arsenal winning a penalty when Kei Kamara pulled Olivier Giroud's shirt and Arteta converted form the spot.
Arsenal was in front inside three minutes, with Alex Oxlade-Chamberlain cut the ball back to Giroud, who went to slide the ball into the net as Sebastien Bassong tried to block him.
There was no uncertainty over the final goal, with Lukas Podolski firing home.
"We left it late, and it was of course unexpected to be 1-0 down at that stage of the game because we were on top and missed chances," Wenger said. "Norwich we knew were strong on set pieces and they punished us for that. We needed spirit and also nerves, we have shown both and in the end got the win we deserved."
It was a routine win for Everton at Goodison Park, with Darron Gibson netting with a deflected strike before half time and a smart finish from Victor Anichebe after the break to leave QPR seven points from safety with just five games remaining.
QPR is only off the bottom because of its superior goal difference over Reading, which ended an eight-game losing run by drawing with Liverpool.
Aston Villa went three points clear of the relegation zone after drawing 1-1 with Fulham, having played two games more than Wigan.
Charles N'Zogbia put Villa in front in the 55th when he bent a shot into the top left of the net, but Fabian Delph flicked a header into his own goal 11 minutes later.
There was also a 1-1 draw in a clash of mid-table Southampton and West Ham.
Andy Carroll ended Southampton's three-match winning run by cancelling out Gaston Ramirez's opener.Suggest a correction