Harry Kane and Andy Keogh struck for Millwall to give Kenny Jackett's side their first home league win of 2012.
On-loan Spurs forward Kane nodded in a header in the first half and Keogh stroked home a penalty in the second after being brought down in the box.
The home side, who have now won 1,000 home games in their history, dominated throughout and should have won by more.
Hull's best chance fell to forward Richard Garcia but his effort was well saved by Maik Taylor.
Nick Barmby's men have now lost five games on the trot in the league, leaving their Championship play-off hopes in tatters, but the victory for the Lions eases their relegation fears and they are now six points clear of the drop zone.
It was an emotional day at the Den, with players and fans paying tribute to former centre-half Barry Kitchener, who died a week ago at the age of 64.
And it was the dogged defending of Shane Lowry and captain Paul Robinson at the heart of the Millwall defence that was key to them keeping a clean sheet as they kept Hull front men Aaron McLean and Garcia quiet for most of the game.
James Henry's corner was bravely headed in by the impressive Kane, who looks set to return to White Hart Lane next season, to open the scoring.
Keogh's late penalty, after he was fouled by Liam Cooper, ensured their first win at home in the league since Boxing Day.