Town Boss Joe Royle claimed that his side were unlucky and the scoreline was misleading: "I cannot remember such a one sided first-half and we should have had a penalty.
"That was a very misleading scoreline. We were guilty of missing a number of really good chances. We were outstanding in that half.
"The second goal was decisive for them because we then had to really go in search of the game.
"The lads said that that goal was offside, but we really should be dealing with those sorts of crosses.
"I don't want to blame the referee too much because I think that apart from the penalty decision he had a really good game."
Meanwhile Millwall assistant manager Ray Wilkins was delighted with the result: "This was a good win for us today because they are probably the best footballing side in the division.
"They played us off the park at stages, but we showed good character to get the result.
"We know that we will give anyone a game on their day and the fact that we have now beaten West Ham, Sunderland and Ipswich proves that.
"I feel for the lads who were taken off. Ifill has been playing well for us recently, but he has gone straight to hospital for a scan."