Goals from Shaun Maloney after 25 minutes and Callum McManaman after 78 minutes allowed Wigan to forget their relegation worries for an afternoon as they finished as deserved winners against the second tier team.
But the match was marred when fighting broke out between Millwall's own fans who traded punches with each other for more than 20 minutes, ignoring their team's efforts on the field.
Eleven fans were arrested and four police officers suffered minor injuries as the skirmishes inside the stadium were shown live to a global television audience and cast a shadow over one of the showpiece occasions of the season, evoking memories of the kind of hooligan violence that blighted English football in the 1970s and 1980s.
Television footage showed several supporters bloodied, police using batons, and a child in tears as the trouble continued.
"The policing response was robust and proportionate and 11 people were arrested during the game in connection with the violence that broke out shortly before half time and full time," the Metropolitan poilice said in a statement. "Four police officers received minor injuries."
The FA called for criminal charges and football banning orders to be brought against those responsible.
Millwall manager Kenny Jackett, in charge of his side for the 300th time, praised his players for their efforts, but said he was unaware of the violence while the match was being played and hence could not comment on the incident.
Wigan manager Roberto Martinez, whose side are two places off the foot of the Premier League table, will meet the winners of Sunday's second semi-final between holders Chelsea and league champions Manchester City when the final is staged back at Wembley on May 11.
They have pulled off some Houdini-like escapes from relegation over the last few seasons, and Martinez said this result would give them heart for the run-in.
"It is a major result for us, you don't usually associate the words Wigan Athletic and FA Cup final in the same sentence," he said.
"Now we must concentrate on the League and make sure we stay up. That is what success will mean to us this season, as well as reaching the cup final."
Saturday's victory represents a major success for Wigan chairman Dave Whelan, who broke his leg playing for Blackburn Rovers in the 1960 FA Cup final against Wolverhampton Wanderers, an injury that finished his top flight career.
He has overseen Wigan's progress from a lower league club to one that has survived in the Premier League since 2005 and although Wigan had hoped he would be able to lead the team out on Saturday, FA protocol did not allow that.
The club is hoping he can do that at the final next month, and Martinez said: "He is a remarkable man. They should make a film of his life for what he has done for Wigan."
WIGAN BREAKTHROUGH
The breakthrough came after 25 minutes following great work in the build-up from Ivorian Arouna Kone, who chested the ball down and then outpaced three men in a powerful run upfield before c
