Maloney gave the Premier League outfit the lead after 25 minutes when he swept in Arouna Kone's lofted cross.
Jordi Gomez and McManaman tested Millwall goalkeeper David Forde before the 2004 finalists responded when a Mark Beevers header was deflected over.
But with 12 minutes left McManaman scored to seal another trip to Wembley.
It was a deserved victory for Wigan who will face either Chelsea or Manchester City, who play their FA Cup semi-final on Sunday.
The game was marred by ugly scenes of Millwall fans fighting during and after the match. The Live TV cameras didn't show most of this but the London club are sure to come under fire as their supporters once again let them down.