Martyn Woolford scored the game's only goal at Craven Cottage as Millwall continued their perfect start to the Championship season.
Holloway told reporters: "We knew it would be tough but we looked sharp and together all the way through. I'm delighted.
"What they spend and what we spend are two different things but you wouldn't have known that.
"The supporters were brilliant, absolutely fantastic. I'm very proud of them."
Millwall continue their season when they face Sheffield Wednesday on Tuesday.