After being largely outplayed in the first half, a rejuvenated Fulham emerged to score within a minute of the restart through their outstanding 17-year-old prospect Ryan Sessegnon.
Ten minutes later, midfielder Kevin McDonald hammered home a fine speculative shot from 25 metres and Aleksandar Mitrovic finished the job with a clinically-taken third in the 89th minute.
It sealed another accomplished victory for Fulham, who have now won 17 of their last 22 league matches in an extraordinary unbeaten sequence.
Slavisa Jokanovic's side also ended Millwall's 17-match unbeaten streak in the league to dent their London rivals' bid to gain promotion from England's second-tier league.
In the battle to earn the second automatic promotion place to the Premier League, with runaway leaders Wolverhampton Wanderers having sealed their spot, Fulham are second on 85 points from 44 games.
The win threw down the gauntlet to Cardiff City, who are on 83 points but the Welsh side have two games in hand, and can regain second spot if they beat Nottingham Forest at home on Saturday.
Millwall retained sixth spot, the last in the playoff zone, on 69 points.
(Reporting by Ian Chadband, editing by Ed Osmond)
